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Professor, Department of Physics and Astronomy<\/p>\n
Email: ealexov@g.clemson.edu<\/p>\n
<\/p>\n
Emil Alexov is a professor of biophysics and bioinformatics in the Department of Physics and Astronomy. He is also Edior-in-Chief of the Journal of Computational Biophysics and Chemistry, and editor for Genes, PLOS Computational Biology and many others. Currently his lab is maintaining and developing DelPhi package for modeling electrostatics in proteins, RNAs and DNAs. Furthermore, his lab developed numerous tools for predicting effect of mutations on protein stability and binding, including protein-DNA binding.<\/p>\n
Dr. Alexov is working to advance personalized medicine and the understanding of molecular mechanisms of human disease in order to more effectively prevent diseases before they even happen.\u00a0 He and his research team look for how DNA variants and other factors cause diseases and identify small molecules (plausible drugs) that bind to dysfunctional mutant protein and restore the wild type function.<\/p>\n
1)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 SK Panday, E Alexov,\u00a0 Protein\u2013Protein Binding Free Energy Predictions with the MM\/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation, ACS omega, 2022<\/p>\n
2)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 G Li, SK Panday, Y Peng, E Alexov, SAMPDI-3D: predicting the effects of protein and DNA mutations on protein\u2013DNA interactions, Bioinformatics 37 (21), 3760-3765, 2021<\/p>\n
3)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 R Aprigliano, ME Aksu, S Bradamante, B Mihaljevic, W Wang, K Rian, Increased p53 signaling impairs neural differentiation in HUWE1-promoted intellectual disabilities, …Cell Reports Medicine 2 (4), 100240, 3,\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 2021<\/p>\n
4)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 G Li, S Pahari, AK Murthy, S Liang, R Fragoza, H Yu, E Alexov, SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein\u2013protein binding affinity, Bioinformatics 37 (7), 992-999, 10\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 2021<\/p>\n
5)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Y Peng, R Kelle, C Little, E Michonova, KG Kornev, E Alexov, pH-dependent interactions of Apolipophorin-III with a lipid disk, Journal of Computational Biophysics and Chemistry 20 (02), 153-164,\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 3, 2021<\/p>\n
6)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 E Alexov, Special Issue on Computational Chemistry Methods to Predict pKa\u2019s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules, Journal of Computational Biophysics and Chemistry 20 (02), 109-110, 2021<\/p>\n
7)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 E Alexov, Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry, Journal of Computational Biophysics and Chemistry 20 (01), 1-1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 , 2021<\/p>\n
8)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 B Wu, W Hand, E Alexov, Opioid addiction and opioid receptor dimerization: structural modeling of the OPRD1 and OPRM1 heterodimer and its signaling pathways, International journal of molecular sciences 22 (19), 10290, 1, 2021<\/p>\n
9)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, HB Shashikala, J Jeffries, B Wu, SK Loftus, JH Zippin, E Alexov, Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease, International journal of molecular sciences 22 (15), 8273, \u00a0\u00a0\u00a0\u00a0 2021<\/p>\n
10)\u00a0\u00a0\u00a0\u00a0\u00a0 S Wang, E Alexov, S Zhao, On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary, Mathematical Biosciences and Engineering 18 (2)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 3, 2021<\/p>\n
11)\u00a0\u00a0\u00a0\u00a0\u00a0 G Li, SK Panday, E Alexov, SAAFEC-SEQ: a sequence-based method for predicting the effect of single point mutations on protein thermodynamic stability, International journal of molecular sciences 22 (2), 606, 18, 2021<\/p>\n
12)\u00a0\u00a0\u00a0\u00a0\u00a0 HBM Shashikala, A Chakravorty, SK Panday, E Alexov, BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics, International Journal of Molecular Sciences 22 (1), 272, \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 1, 2020<\/p>\n
13)\u00a0\u00a0\u00a0\u00a0\u00a0 SR Ganakammal, M Koirala, B Wu, E Alexov, In-silico analysis to identify the role of MEN1 missense mutations in breast cancer, Journal of Theoretical and Computational Chemistry 19 (06), 2041002, 3\u00a0\u00a0\u00a0\u00a0\u00a0 2020<\/p>\n
14)\u00a0\u00a0\u00a0\u00a0\u00a0 E Alexov, An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants. Genes 11 (9), 2020<\/p>\n
15)\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, E Alexov, Computational chemistry methods to investigate the effects caused by DNA variants linked with disease, Journal of Theoretical and Computational Chemistry 19 (06), 1930001, 1, 2020<\/p>\n
16)\u00a0\u00a0\u00a0\u00a0\u00a0 S Ranganathan Ganakammal, E Alexov, An ensemble approach to predict the pathogenicity of synonymous variants, Genes 11 (9), 1102, 4, 2020<\/p>\n
17)\u00a0\u00a0\u00a0\u00a0\u00a0 YR Lee, K Khan, K Armfield-Uhas, S Srikanth, NA Thompson, M Pardo, Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy, …Nature communications 11 (1), 1-17, 17, 2020<\/p>\n
18)\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, E Alexov, Ab-initio binding of barnase\u2013barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach, Journal of Theoretical and Computational Chemistry 19 (04), 2050016.<\/p>\n
19)\u00a0\u00a0\u00a0\u00a0\u00a0 C Li, M McGowan, E Alexov, S Zhao, A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation, Mathematical Biosciences and Engineering 17 (6).<\/p>\n
20)\u00a0\u00a0\u00a0\u00a0\u00a0 S Wang, A Lee, E Alexov, S Zhao. A regularization approach for solving Poisson\u2019s equation with singular charge sources and diffuse interfaces. Applied Mathematics Letters 102, 106144<\/p>\n
21)\u00a0\u00a0\u00a0\u00a0\u00a0 A Chakravorty, S Panday, S Pahari, S Zhao, E Alexov. Capturing the effects of explicit waters in implicit electrostatics modeling: Qualitative justification of Gaussian-based dielectric models in DelPhi. Journal of Chemical Information and Modeling<\/p>\n
22)\u00a0\u00a0\u00a0\u00a0\u00a0 S Pahari, G Li, AK Murthy, S Liang, R Fragoza, H Yu, E Alexov. SAAMBE-3D: Predicting Effect of Mutations on Protein\u2013Protein Interactions. International journal of molecular sciences 21 (7), 2563<\/p>\n
23)\u00a0\u00a0\u00a0\u00a0\u00a0 SR Ganakammal, E Alexov. Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants. PeerJ 7, e8106<\/p>\n
24)\u00a0\u00a0\u00a0\u00a0\u00a0 SK Panday, MHB Shashikala, M Koirala, S Pahari, A Chakrvorty, Y Peng, …E. Alexov. Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]. Living Journal of Computational Molecular Science 1 (2), 10841C<\/p>\n
25)\u00a0\u00a0\u00a0\u00a0\u00a0 Li, Z Jia, A Chakravorty, S Pahari, Y Peng, S Basu, M Koirala, \u2026 E. Alexov. DelPhi Suite: New Developments and Review of Functionalities. Journal of Computational Chemistry 40 (28), 2502-2508<\/p>\n
26)\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, E Alexov. Computational chemistry methods to investigate the effects caused by DNA variants linked with disease. Journal of Theoretical and Computational Chemistry, 1930001.<\/p>\n
27)\u00a0\u00a0\u00a0\u00a0\u00a0 T Hazra, SA Ullah, S Wang, E Alexov, S Zhao. A super-Gaussian Poisson\u2013Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.\u00a0 Journal of mathematical biology 79 (2), 631-672<\/p>\n
28)\u00a0\u00a0\u00a0\u00a0\u00a0 N Tajielyato, E Alexov. Modeling pKas of unfolded proteins to probe structural models of unfolded state.\u00a0 Journal of Theoretical and Computational Chemistry 18 (04), 1950020<\/p>\n
29)\u00a0\u00a0\u00a0\u00a0\u00a0 Spellicy CJ, Peng Y, Olewiler L, Cathey SS, Rogers RC, Bartholomew D, Johnson J, Alexov E, Lee JA, Friez MJ, Jones JR. Three additional patients with EED-associated overgrowth: potential mutation hotspots identified? J Hum Genet. 2019 Mar 11. doi: 10.1038\/s10038-019-0585-5.<\/p>\n
30)\u00a0\u00a0\u00a0\u00a0\u00a0 Tajielyato N, Alexov E. Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. Int J Mol Sci. 2019 Mar 3;20(5). pii: E1090. doi: 10.3390\/ijms20051090.<\/p>\n
31)\u00a0\u00a0\u00a0\u00a0\u00a0 Pahari S, Sun L, Alexov E. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database (Oxford). 2019 Jan 1;2019. pii: baz024. doi: 10.1093\/database\/baz024.<\/p>\n
32)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Gallicchio E, Alexov E. A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. J Comput Chem. 2019 May 5;40(12):1290-1304. doi: 10.1002\/jcc.25786. Epub 2019 Jan 30.<\/p>\n
33)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci. 2019 Jan 28;20(3). pii: E548. doi: 10.3390\/ijms20030548.<\/p>\n
34)\u00a0\u00a0\u00a0\u00a0\u00a0 Pahari S, Sun L, Basu S, Alexov E. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins. 2018 Dec;86(12):1277-1283. doi: 10.1002\/prot.25608. Epub 2018 Oct 26<\/p>\n
35)\u00a0\u00a0\u00a0\u00a0\u00a0 Tajielyato N, Li L, Peng Y, Alper J, Alexov E. E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein. Sci Rep. 2018 Sep 5;8(1):13266. doi: 10.1038\/s41598-018-31480-9.<\/p>\n
36)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Jia Z, Peng Y, Tajielyato N, Wang L, Alexov E. Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents. Front Mol Biosci. 2018 Mar 27;5:25. doi: 10.3389\/fmolb.2018.00025<\/p>\n
37)\u00a0\u00a0\u00a0\u00a0\u00a0 Spellicy CJ, Norris J, Bend R, Bupp C, Mester P, Reynolds T, Dean J, Peng Y, Alexov E, Schwartz CE, Stevenson RS, J Friez M. Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects. Eur J Hum Genet. 2018 Mar;26(3):420-427.<\/p>\n
38)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Jia Z, Li L, Zhao S, Alexov E. Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling. J Chem Theory Comput. 2018 Feb 13;14(2):1020-1032. doi: 10.1021\/acs.jctc.7b00756. Epub 2018 Feb 3.<\/p>\n
39)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Myers R, Zhang W, Alexov E. Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome. Int J Mol Sci. 2018 Jan 4;19(1). pii: E141. doi: 10.3390\/ijms19010141.<\/p>\n
40)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Sun L, Jia Z, Li L, Alexov E. Predicting protein-DNA binding free energy change upon missense mutations using modified MM\/PBSA approach: SAMPDI webserver. Bioinformatics. 2018 Mar 1;34(5):779-786. doi: 10.1093\/bioinformatics\/btx698.<\/p>\n
41)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E. DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinformatics. 2017 Nov 15;33(22):3661-3663. doi: 10.1093\/bioinformatics\/btx495<\/p>\n
42)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Jia Z, Peng Y, Godar S, Getov I, Teng S, Alper J, Alexov E. Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. Sci Rep. 2017 Aug 15;7(1):8237. doi: 10.1038\/s41598-017-08419-7.<\/p>\n
43)\u00a0\u00a0\u00a0\u00a0\u00a0 Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem. 2017 Aug 15;38(22):1974-1979. doi: 10.1002\/jcc.24831.<\/p>\n
44)\u00a0\u00a0\u00a0\u00a0\u00a0 Hoffman L, Li L, Alexov E, Sanabria H, Waxham MN. Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner. Biochemistry. 2017 Mar 24. doi: 10.1021\/acs.biochem.7b00028<\/p>\n
45)\u00a0\u00a0\u00a0\u00a0\u00a0 Vaidyanathan K, Niranjan T, Selvan N, Teo CF, May M, Patel S, Weatherly B, Skinner C, Opitz J, Carey J, Viskochil D, Gecz J, Shaw M, Peng Y, Alexov E, Wang T, Schwartz C, Wells L. Identification and Characterization of a Missense Mutation in the O-GlcNAc Transferase Gene that Segregates with X-Linked Intellectual Disability. J Biol Chem. 2017 Mar 16. pii: jbc.M116.771030. doi: 10.1074\/jbc.M116.771030<\/p>\n
46)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Jia Z, Li L, Alexov E. A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential. Langmuir. 2017 Feb 20. doi: 10.1021\/acs.langmuir.6b04430. [Epub ahead of print]. PMID: 28181811<\/p>\n
47)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Chakravorty A, Alexov E. DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem. 2017 Apr 5;38(9):584-593. doi: 10.1002\/jcc.24715. PMID: 28130775<\/p>\n
48)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E. Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes. Proteins. 2017 Feb;85(2):282-295. doi: 10.1002\/prot.25221. PMID: 27936518<\/p>\n
49)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E. Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. Proteins. 2016 Dec;84(12):1797-1809. doi: 10.1002\/prot.25162. PMID: 27696497<\/p>\n
50)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakavorty A, Li L, Alexov E. Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. J Comput Chem. 2016 Aug 21. doi: 10.1002\/jcc.24475. PMID: 27546093<\/p>\n
51)\u00a0\u00a0\u00a0\u00a0\u00a0 Yang Y, Kucukkal TG, Li J, Alexov E, Cao W. Binding Analysis of Methyl-CpG Binding Domain of MeCP2 and Rett Syndrome Mutations. ACS Chem Biol. 2016 Oct 21;11(10):2706-2715. Epub 2016 Aug 8. PMID: 27356039<\/p>\n
52)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Dai L, Alexov E. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations. Int J Mol Sci. 2016 Apr 12;17(4). pii: E547. doi: 10.3390\/ijms17040547. PMID: 27077847<\/p>\n
53)\u00a0\u00a0\u00a0\u00a0\u00a0 Getov I, Petukh M, Alexov E. SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM\/PBSA Approach.\u00a0 Int J Mol Sci. 2016 Apr 7;17(4). pii: E512. doi: 10.3390\/ijms17040512. PMID: 27070572<\/p>\n
54)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Alper J, Alexov E. Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Sci Rep. 2016 Mar 18;6:23249. doi: 10.1038\/srep23249. PMID:\u00a0 26988596<\/p>\n
55)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Norris J, Schwartz C, Alexov E. Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase. Int J Mol Sci. 2016 Jan 8;17(1). pii: E77. doi: 10.3390\/ijms17010077. PMID:\u00a0 26761001<\/p>\n
56)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E., Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. Proteins. 2015 Dec 9. doi: 10.1002\/prot.24968. [Epub ahead of print], PMID: 26650512<\/p>\n
57)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Suryadi J, Yang Y, Kucukkal TG, Cao W, Alexov E., Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease, Int J Mol Sci. 2015 Nov 13;16(11):27270-87. doi: 10.3390\/ijms161126022.<\/p>\n
58)\u00a0\u00a0\u00a0\u00a0\u00a0 Wang L, Zhang M, Alexov E., DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs, Bioinformatics. 2015 Oct 29. pii: btv607.<\/p>\n
59)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Zhang M, Alexov E., Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence, J Comput Chem. 2015 Oct 20. doi: 10.1002\/jcc.24218.<\/p>\n
60)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Yang Y, Uvarov O, Cao W, Alexov E., Impact of Rett Syndrome Mutations on MeCP2 MBD Stability, Biochemistry. 2015 Oct 20;54(41):6357-68. doi: 10.1021.<\/p>\n
61)\u00a0\u00a0\u00a0\u00a0\u00a0 Wang L, Li L, Alexov E., pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa, Proteins. 2015 Sep 26. doi: 10.1002\/prot.24935.<\/p>\n
62)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Li M, Alexov E, Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM\/PBSA Method, PLoS Comput Biol. 2015 Jul 6;11(7):e1004276. doi: 10.1371.<\/p>\n
63)\u00a0\u00a0\u00a0\u00a0\u00a0 Emil Alexov \u201cAdvances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine, Advances in Biology 2015, ID 471836<\/p>\n
64)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Alexov E., Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2, Comput Math Methods Med. 2015;2015:746157. doi: 10.1155<\/p>\n
65)\u00a0\u00a0\u00a0\u00a0\u00a0 May M, Hwang KS, Miles J, Williams C, Niranjan T, Kahler SG, Chiurazzi P, Steindl K, Van Der Spek PJ, Swagemakers S, Mueller J, Stefl S, Alexov E, Ryu JI, Choi JH, Kim HT, Tarpey P, Neri G, Holloway L, Skinner C, Stevenson RE, Dorsky RI, Wang T, Schwartz CE, Kim CH, ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons, Hum Mol Genet. 2015 Sep 1;24(17):4848-61. doi: 10.1093.<\/p>\n
66)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Wang L, Alexov E., On the energy components governing molecular recognition in the framework of continuum approaches, Front Mol Biosci. 2015 Mar 6;2:5. doi: 10.3389<\/p>\n
67)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Alexov E., Ion binding to biological macromolecules, Asian J Phys. 2014 Nov;23(5):735-744.<\/p>\n
68)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Kucukkal TG, Alexov E., On human disease-causing amino acid variants: statistical study of sequence and structural patterns, Hum Mutat. 2015 May;36(5):524-34. doi: 10.1002<\/p>\n
69)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Petukh M, Li L, Alexov E., Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins, Curr Opin Struct Biol. 2015 Jun;32:18-24. doi: 10.1016.<\/p>\n
70)\u00a0\u00a0\u00a0\u00a0\u00a0 Campbell B, Petukh M, Alexov E, Li C., On the electrostatic properties of homodimeric proteins, J Theor Comput Chem. 2014;13(3).<\/p>\n
71)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Wu B, Stefl S, Smith N, Hyde-Volpe D, Wang L, Alexov E., Chronic Beryllium Disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2, PLoS One. 2014 Nov 4;9(11):e111604.<\/p>\n
72)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Martiny V, Lagorce D, Ikeguchi Y, Alexov E, Miteva MA., Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach, PLoS One. 2014 Oct 23;9(10):e110884.<\/p>\n
73)\u00a0\u00a0\u00a0\u00a0\u00a0 Kimmett T, Smith N, Witham S, Petukh M, Sarkar S, Alexov E., ProBLM web server: protein and membrane placement and orientation package, Comput Math Methods Med. 2014;2014:838259.<\/p>\n
74)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Li C, Alexov E., On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function, J Theor Comput Chem. 2014 May;13(3).<\/p>\n
75)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Yang Y, Chapman SC, Cao W, Alexov E., Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics, Int J Mol Sci. 2014 May 30;15(6):9670-717<\/p>\n
76)\u00a0\u00a0\u00a0\u00a0\u00a0 Li M, Petukh M, Alexov E, Panchenko AR., Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity, J Chem Theory Comput. 2014 Apr 8;10(4):1770-1780<\/p>\n
77)\u00a0\u00a0\u00a0\u00a0\u00a0 Dias RP, Li L, Soares TA, Alexov E., Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi, J Comput Chem. 2014 Jul 15;35(19):1418-29.<\/p>\n
78)\u00a0\u00a0\u00a0\u00a0\u00a0 Nedumpully-Govindan P, Li L, Alexov EG, Blenner MA, Ding F., Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity, Bioinformatics. 2014 Aug 15;30(16):2302-9.<\/p>\n
79)\u00a0\u00a0\u00a0\u00a0\u00a0 Alexov E, Sternberg M., Understanding molecular effects of naturally occurring genetic differences, J Mol Biol. 2013 Nov 1;425(21):3911-3.<\/p>\n
80)\u00a0\u00a0\u00a0\u00a0\u00a0 Onufriev AV, Alexov E., Protonation and pK changes in protein-ligand binding. Q Rev Biophys. 2013 May;46(2):181-209.<\/p>\n
81)\u00a0\u00a0\u00a0\u00a0\u00a0 Boccuto L, Aoki K, Flanagan-Steet H, Chen CF, Fan X, Bartel F, Petukh M, Pittman A, Saul R, Chaubey A, Alexov E, Tiemeyer M, Steet R, Schwartz CE. \u201cA mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation\u201d, Hum Mol Genet. 2013 Sep 26.<\/p>\n
82)\u00a0\u00a0\u00a0\u00a0\u00a0 Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E \u201cMolecular Mechanisms of Disease-Causing Missense Mutations\u201d, J Mol Biol. 2013 Jul 16. doi:pii: S0022-2836(13)00446-4. 10.1016\/j.jmb.2013.07.014. [Epub ahead of print]<\/p>\n
83)\u00a0\u00a0\u00a0\u00a0\u00a0 Dolzhanskaya N, Gonzalez M, Stefl S, Messing J, Wen GY, Alexov E, Zuchner S, Velinov M \u201cA novel Leu(381)Phe mutation in Presenilin 1 is associated with very early onset and unusually fast progressing dementia, and lysosomal inclusions typically seen in Kufs disease\u201d, Journal of Alzheimer’s Disease, 2014;39(1):23-7. doi: 10.3233<\/p>\n
84)\u00a0\u00a0\u00a0\u00a0\u00a0 Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR. \u201cCancer missense mutations alter binding properties of proteins and their interaction networks\u201d, PLoS One. 2013 Jun 14;8(6):e66273.<\/p>\n
85)\u00a0\u00a0\u00a0\u00a0\u00a0 Li C, Petukh M, Li L, Alexov E. \u201cContinuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi\u201d, J Comput Chem. 2013 Jun 4. doi: 10.1002\/jcc.23340.<\/p>\n
86)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Norris J, Kalscheuer V, Wood T, Wang L, Schwartz C, Alexov E, Van Esch H. \u201cA Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome\u201d, Hum Mol Genet. 2013 May 31.<\/p>\n
87)\u00a0\u00a0\u00a0\u00a0\u00a0 Chuan Li, Lin Li, Marharyta Petukh and Emil Alexov; “Progress in developing Poisson-Boltzmann equation solvers”; Molecular Based Mathematical Biology. 2013, Volume 1, Pages 42-62.<\/p>\n
88)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Li C, Zhang Z, Alexov E.; “On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi”; J Chem Theory Comput. 2013 Apr 9;9(4):2126-2136.<\/p>\n
89)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E. “Enhancing human spermine synthase activity by engineered mutations.” PLoS Comput Biol. 2013 Feb;9(2):e1002924. doi:10.1371\/journal.pcbi.1002924. Epub 2013 Feb 28. Figure 2 of the manuscript is taken for the cover page of the journal<\/p>\n
90)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Witham S, Petukh M, Moroy G, Miteva M, Ikeguchi Y, Alexov E. “A rational free energy-based approach to understanding and targeting disease-causing missense mutations.” J Am Med Inform Assoc. 2013 Feb 13. [Epub ahead of print]<\/p>\n
91)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Kimmet T, Alexov E. “BION web server: predicting non-specifically bound surface ions.” Bioinformatics. 2013 Mar 15;29(6):805-6<\/p>\n
92)\u00a0\u00a0\u00a0\u00a0\u00a0 Smith N, Campbell B, Li L, Li C, Alexov E. “Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.” BMC Struct Biol. 2012 Dec 5;12:31. doi:10.1186\/1472-6807-12-31.<\/p>\n
93)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Stefl S, Alexov E “The Role of Protonation States in Ligand Receptor Recognition and Binding.” Curr Pharm Des. 2012 Nov 20. [Epub ahead of print]<\/p>\n
94)\u00a0\u00a0\u00a0\u00a0\u00a0 Takano K, Lieu D, Tarpey P, Gallant E, Lam A, Witham S, Alexov E, Chaubey A, Stevenson RE, Schwartz CE, Board PG, Dulhunty AF “An X-linked Channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity”, Hum Mol Genet. 2012 Aug Oct 15;21(20):4497-507. Epub 2012 Jul 19.<\/p>\n
95)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Zhenirovskyy M, Li C, Li L, Wang L, Alexov E. “Predicting nonspecific ion binding using Delphi”, Biophys J. 2012 Jun 20, 102(12)<\/p>\n
96)\u00a0\u00a0\u00a0\u00a0\u00a0 Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia and Emil Alexov “DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes”, Comm. Comp. Phys., (2013), 13, 269-84<\/p>\n
97)\u00a0\u00a0\u00a0\u00a0\u00a0 Lin Wang, Shawn Witham, Zhe Zhang, Lin Li, Michael Hodsdon and Emil Alexov “In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor”, Comm. Comp. Phys., (2013), 13, 207-222<\/p>\n
98)\u00a0\u00a0\u00a0\u00a0\u00a0 Lin Wang, Zhe Zhang, Walter Rocchia and Emil Alexov “Using DelPhi capabilities to mimic protein\u2019s conformational reorganization with amino acid specific dielectric constants”, Comm. Comp. Phys., (2013), 13, 13-30<\/p>\n
99)\u00a0\u00a0\u00a0\u00a0\u00a0 Sergio Decherchi, Jos\u00b4e Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, and Walter Rocchia “Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution”, Comm. Comp. Phys., (2013), 13, 61-89<\/p>\n
100)\u00a0\u00a0\u00a0 Li C, Li L, Zhang J, Alexov E., “Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi.”, J Comput Chem. 2012 Sep 15;33(24):1960-6. doi: 10.1002\/jcc.23033. Epub 2012 Jun 4.; Figure 3 of the manuscript is the cover page of the journal: J Comput Chem. 2012 Sep 15;33(24):iii-iv. doi:10.1002\/jcc.22080<\/p>\n
101)\u00a0\u00a0\u00a0 Zhe Zhang, Maria A. Miteva, Lin Wang and Emil Alexov “Analyzing Effects of Naturally Occurring Missense Mutations” Computational and Mathematical Methods in Medicine, Volume 2012 (2012), Article ID 805827, doi:10.1155\/2012\/805827<\/p>\n
102)\u00a0\u00a0\u00a0 Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z, Wang L, Smith N, Petukh M, Alexov E. “DelPhi: a comprehensive suite for DelPhi software and associated resources.” BMC, Biophys, (2012) May14;4(1):9.<\/p>\n
103)\u00a0\u00a0\u00a0 Nicholas Smith, Subhra Sarkar, Shawn Witham, Jie Zhang, Lin Li, Chuan Li and Emil Alexov “DelPhi Web Server v2: Incorporating atomic-style geometrical figures into the computational protocol”, Bioinformatics (2012), 28(12):1655-7.<\/p>\n
104)\u00a0\u00a0\u00a0 Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E, “Predicting folding free energy changes upon single point mutations”, Bioinformatics, (2012), 28(5):664-71.<\/p>\n
105)\u00a0\u00a0\u00a0 Mitra, R., Zhang. Zhe and Alexov, E, “In silico modeling of pH-optimum of protein-protein binding”, Proteins (2011), 171, 285-289.<\/p>\n
106)\u00a0\u00a0\u00a0 Zhang, Zhe, Witham, S. and Alexov, E., “On the role of electrostatics on protein-protein interactions”, Physical Biology 2011 Jun;8(3):035001. Epub 2011 May 13.<\/p>\n
107)\u00a0\u00a0\u00a0 Zhang, Zhe, Norris, J., Schwartz, C. and Alexov, E. “In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in Spermine Synthase”, PLoS One, (2011);6(5):e20373.<\/p>\n
108)\u00a0\u00a0\u00a0 Witham, S., Takano, K., Schwartz, C. and Alexov, E. “A Missense Mutation in CLIC2 Associated with Intellectual Disability is Predicted by In Silico Modeling to Affect Protein Stability and Dynamics”, Proteins, (2011) 79(8):2444-54. doi: 10.1002\/prot.23065.<\/p>\n
109)\u00a0\u00a0\u00a0 Alexov, E., Mehler, E.L., Baker, N., Baptista, A.M., Huang, Y., Milletti, F., Nielsen, J.E., Farrell, D., Carstensen, T., Olsson, M.H.M., Shen, J.K., Warwicker, J., Williams, S., and Word, J.M., “Progress in the prediction of pKa values in proteins”, Proteins, (2011), 79(12):3260-75, doi:10.1002\/prot.23189.<\/p>\n
110)\u00a0\u00a0\u00a0 Teng S, Srivastava AK, Schwartz CE, Alexov E, Wang L , \u201cStructural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interactions\u201d, Int J Comput Biol Drug Des. 2011;3(4):334-49.<\/p>\n
111)\u00a0\u00a0\u00a0 Mitra, R., Zhang. Zhe and Alexov, E, \u201cIn silico modeling of pH-optimum of protein\u2013protein binding\u201d, Proteins (2011), 171, 285-289.<\/p>\n
112)\u00a0\u00a0\u00a0 Talley, K. and Alexov, E. \u201cOn the pH-optimum of activity and stability\u201d, Proteins (2010), 78, 2699-706.<\/p>\n
113)\u00a0\u00a0\u00a0 Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E. \u201cComputational analysis of missense mutations causing Snyder-Robinson syndrome\u201d, Hum Mutat. (2010) 31(9):1043-9.<\/p>\n
114)\u00a0\u00a0\u00a0 Mitra, R. and Alexov, E.\u00a0 \u201cAnalyzing and Predicting Protein Binding Pockets In Silico Lead Discovery, 2011, 84-98.<\/p>\n
115)\u00a0\u00a0\u00a0 Teng, S., Madej, T., Panchenko, A. and Alexov, E. \u201cModeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions\u201d, Biophysical Journal, (2009), 96, 2178-2188.<\/p>\n
116)\u00a0\u00a0\u00a0 Talley Kemper, Ng Carmen, Snoppell Michael, Kundrotas Petras and Alexov E.\u00a0 “On the electrostatic component of protein-protein binding free energy\u201d\u00a0 PMC Biophysics 2008,1:2\u00a0 1-23.<\/p>\n
117)\u00a0\u00a0\u00a0 Kosloff M., Alexov E., Arshavsky Y. and Hong B. “Electrostatic and Lipid Anchor Contributions to the Interaction of Transduin with Membrane\u201d\u00a0 The Journal of Biological Chemistry 283(2008)\u00a0 31197-31207.<\/p>\n
118)\u00a0\u00a0\u00a0 Mitra, R, Shyam, R., Mitra, I., Miteva, M. and Alexov, E \u201cCalculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions\u201d Current Computer-Aided Drug Design: 4: 169-179.<\/p>\n
119)\u00a0\u00a0\u00a0 Kundrotas, P, Lensink, M. and Alexov, E. \u201cHomology-based modeling of 3D structures of protein-protein complexes using alignment of modified sequence profiles\u201d, Int. J. Biol. Macromol. (2008), 43: 198-208.<\/p>\n
120)\u00a0\u00a0\u00a0 Alexov, E.\u00a0 \u201c Editorial\u201d,\u00a0\u00a0 Current Pharmaceutical Biotechnology (2008) 9:55-56.<\/p>\n
121)\u00a0\u00a0\u00a0 Miteva, A.Maria, Alexov , Emil, Villoutreix, Bruno.O\u00a0 “Protein Structure Analysis Online\u201d\u00a0 Current Protocols in Protein Science (2007)\u00a0 2:13:1-23.<\/p>\n
122)\u00a0\u00a0\u00a0 Teng S., Michonova-Alexova E and Alexov, E.\u00a0 “Approaches and Resources for prediction of the Effects of Non-Synonymous Single Nucleotide Polymorphism on Protein Function and Intearctions\u201d\u00a0 Current Pharmaceutical Biotechnology (2008) 9:123-133.<\/p>\n
123)\u00a0\u00a0\u00a0 Talley, K., Kundrotas, P. and Alexov, E. \u201cModeling Salt Dependence of Protein-Protein Association: Linear vs Non-Linear Poisson-Boltzmann Equation\u201d. Comm. Comp. Phys. (2008), 3: 1071.<\/p>\n
124)\u00a0\u00a0\u00a0 Kundrotas P. and Alexov E. \u201cPredicting interacting and interfacial residues using continuous sequence segments\u201d Int J Biol Macromol. 2007 Dec 1;41(5):615-23. Epub 2007 Aug 9.<\/p>\n
125)\u00a0\u00a0\u00a0 Brook K., Talley. K., Coley. K., Kundrotas P., Alexov. E. \u201cOptimization of electrostatic interactions in protein-protein complexes\u201d. Biophys J. 2007 Nov 15;93(10):3340-52. Epub 2007 Aug 10.<\/p>\n
126)\u00a0\u00a0\u00a0 Augustin Ofiretu, Nadia Bucurenci, Emil Alexov, Thomas Bertrand, Pierre Briozzo, Helene Munier-Lehmann and Anne-Marie Gilles \u201cStructural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase\u201d, FEBS Letters (2007) 274, 3363\u20133373.<\/p>\n
127)\u00a0\u00a0\u00a0 Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. \u201cAssessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families \u201d J. Bioinformatics and Comp. Biol.\u00a0 (2007), 5, 693-715.<\/p>\n
128)\u00a0\u00a0\u00a0 Kundrotas, P., Georgieva, P., Shosheva, A., Christova, P. and Alexov, E. \u201cBANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families\u201d, Int. J. Biol. Macromol.(2007), Jun 1;41(1):114-9.<\/p>\n
129)\u00a0\u00a0\u00a0 C. L. Tang, E. Alexov, A. Pyle and B. Honig \u201cCalculation of pKas in RNA: On the structural origins and functional roles of protonated nucleotides\u201d, J. Mol. Biol. (2007), Mar 9; 366(5):1475-96.<\/p>\n
130)\u00a0\u00a0\u00a0 Claudia, B., Honig, B. and Alexov, E. \u201cPoisson-Boltzmann calculations of non-specific salt effects on protein-protein binding free energies\u201d, Biophys. J. (2007), Mar 15; 92(6):1891-9.<\/p>\n
131)\u00a0\u00a0\u00a0 Isvoran, A., Craescu, C. and Alexov, E. \u201cElectrostatic control of the overall shape of calmodulin: numerical calculations\u201d Eur. Biophys. J (2007) Mar; 36(3):225-37.<\/p>\n
132)\u00a0\u00a0\u00a0 Kundrotas, P.J. and\u00a0 Alexov, E. \u201cPredicting residue contacts using pragmatic correlated mutations method: reducing the false positives\u201d BMC Bioinformatics, 2006. 7(1): p. 503.<\/p>\n
133)\u00a0\u00a0\u00a0 Kundrotas, P. and Alexov, E \u201cProtCom: Searchable database of protein-protein complexes\u201d Nuclear Acids Research (2007) 35. D575-D579.<\/p>\n
134)\u00a0\u00a0\u00a0 Kundrotas, P. and Alexov, E \u201cPredicting 3D structures of transient protein-protein complexes by homology\u201d Biochimica at Biophysica Acta\u00a0 (2006), 1764, 1498-1511.<\/p>\n
135)\u00a0\u00a0\u00a0 Kundrotas, P. and Alexov, E \u201cElectrostatic properties of protein-protein complexes\u201d Biophys. J. (2006), 91, 1724-1736.<\/p>\n
136)\u00a0\u00a0\u00a0 Wu Y, Hudson JS, Lu Q, Moore JM, Mount AS, Rao AM, Alexov E, Ke PC. \u201cCoating single-walled carbon nanotubes with phospholipids\u201d,\u00a0 J Phys Chem B (2006), 110(6):2475-2478.<\/p>\n
137)\u00a0\u00a0\u00a0 Grey MJ, Tang Y, Alexov E, McKnight CJ, Raleigh DP, Palmer AG 3rd. \u201cCharacterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain\u201d J Mol Biol (2006) 355:1078-1094.<\/p>\n
138)\u00a0\u00a0\u00a0 Shosheva, A., Donchev, A., Dimitrov, M., Kostov, G., Toromanov, G., Getov, V and E. Alexov \u201cComparative study of the stability of poplar plastocyanin isoforms\u201d Biochimica et Biophysica Acta (2005), 1748, 116-127<\/p>\n
139)\u00a0\u00a0\u00a0 Zhu, J., Alexov, E. and B. Honig \u201cComparative Study of Generalized Born Models: Born Radii and Peptide Folding\u201d J. Phys. Chem. B (2005) 109, 3008-3022.<\/p>\n
140)\u00a0\u00a0\u00a0 Alexov, E. \u201cCalculating Proton Uptake\/Release and Binding Free Energy Taking into Account Ionization and Conformation Changes Induced by Protein-Inhibitor Association: Application to Plasmepsin, Cathepsin D and Endothiapepsin-Pepstatin complexes\u201d Proteins (2004), 56, 572-584.<\/p>\n
141)\u00a0\u00a0\u00a0 Tang C., Xie L., Koh I., Posy S., Alexov E. and Honig B. \u201cOn the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles\u201d J. Mol. Biol. (2003), 334, 1043-1062.<\/p>\n
142)\u00a0\u00a0\u00a0 Shosheva, A., Donchev, A., Dimitrov, M., Zlatanav, I., Toromanov, G., Getov, V. and Alexov, E. \u201cExperimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity\u201d Biochemica at Biophysica Acta\u00a0 (2004), 1698, 67-75.<\/p>\n
143)\u00a0\u00a0\u00a0 Alexov, E. \u201cNumerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure\u201d Eur. J. Biochem. (2004), 271, 173-185.<\/p>\n
144)\u00a0\u00a0\u00a0 Petrey D., Xiang Z., Tang C., Xie. L., Gimpelev M., Mitros T., Soto C., Golgsnith-Fischman S., Kernytsky A., Schlessinger A., Koh I., Alexov E. and Honig B.\u00a0 \u201cUsing Multiple Structure Alignment, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling\u201d Proteins (2003), 53, 430-435.<\/p>\n
145)\u00a0\u00a0\u00a0 Alexov, E. \u201cRole of the Protein Side-Chain Fluctuations on the Strength of Pair-Wise Electrostatic Interactions: Comparing Experimental with Computed pKa\u2019s\u201d, Proteins (2003), 50, 94-103.<\/p>\n
146)\u00a0\u00a0\u00a0 Georgescu, R., Alexov, E. and Gunner M. \u201cCombining Conformational Flexibility and Continuum Electrostatics for Calculating pKa\u2019s in Proteins\u201d Biophys. J. (2002), 83, 1731-1748.<\/p>\n
147)\u00a0\u00a0\u00a0 J. Tandory, P. Maroti, E. Alexov, P. Sebban and L. Baciou \u201cKey role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides\u201d PNAS (2002), 99, 6702-6706.<\/p>\n
148)\u00a0\u00a0\u00a0 J. Tandory, L. Baciou, E. Alexov, P. Maroti, M. Schiffer, D. Hanson and P. Sebban \u201cRevealing the Involvement of Extended Hydrogen Bond Networks in the Cooperative Function between Distant Sites in Bacterial Reaction Center\u201d, J. Biol. Chem. (2001), 276, 45513-45515.<\/p>\n
149)\u00a0\u00a0\u00a0 Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A. and Honig, B. \u201c Rapid grid-based Construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: application to the molecular systems and geometrical objects\u201d, J. Comp. Chem. (2002), 23, 1-10.<\/p>\n
150)\u00a0\u00a0\u00a0 Alexov, E. and Honig, B. \u201cStructural and Energetic Basis of Molecular Recognition\u201d in Handbook of Cell Signaling (2002), R. Bradshaw and E. A. Dennis, Editors, Academic Press, San Diego, CA. p.11-13.<\/p>\n
151)\u00a0\u00a0\u00a0 Rocchia, W., Alexov, E. and Honig, B. \u201cExtending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions\u201d, J. Phys. Chem. (2001), 105, 6507-6514.<\/p>\n
152)\u00a0\u00a0\u00a0 Alexov, E., Valerio-Lepinies, M., Baciou, L., Schiffer, M., Hadson, D.K, Sebban, P. and Gunner, M. “Modeling the effects of mutations within QB pocket in reaction center proteins”, Biochemistry\u00a0 (2000), 39, 5940-5952.<\/p>\n
153)\u00a0\u00a0\u00a0 Gunner, M. and Alexov, E.” A pragmatic approach to structure based calculations of coupled proton and electron transfer in proteins”, Biochimica at Biophysica Acta (2000), 44819 , 1-25.<\/p>\n
154)\u00a0\u00a0\u00a0 Alexov, E. and Gunner, M. “Calculating protein and proton motions coupled to electron transfer: The electron transfer from QA to QB in photosynthetic reaction centers from Rb. Sphaeroides”, Biochemistry, (1999), 38 (26) 8253-8270.<\/p>\n
155)\u00a0\u00a0\u00a0 Miteva, M. , Alexov , E. and Atanasov, B. Numerical simulation of aldolase tetramer stability, Eur. Biophys. J.\u00a0 (1998), 28, 67-73.<\/p>\n
156)\u00a0\u00a0\u00a0 Gunner, M.R. and Alexov, E. (1997) The role of the protein in modulating cofactor electrochemistry in proteins: The calculation of electrostatic forces. Molecular modeling and dynamics of bioinorganic systems. Dordrecht, Kluwer. (L. Banci and P. Comba ed.) 361-390.<\/p>\n
157)\u00a0\u00a0\u00a0 Gunner, R., Alexov, E., Torres E and Lipovaca S. The importance of the protein in controlling the electrochemistry of heme metalloproteins. Methods of calculation and analysis. J. Biol. Phys. Chem.\u00a0 (1997), 2, 126-134<\/p>\n
158)\u00a0\u00a0\u00a0 Alexov, E.G. & Gunner, M.R. “Including protein conformational flexibility into the calculation of\u00a0 pH-dependent protein properties”, Biophys. J.\u00a0 (1997) 74, 2075-2093<\/p>\n
159)\u00a0\u00a0\u00a0 Alexov, E. ,Atanasov, B. “Selective absorption of radio frequency energy due to collective motion of charged domains: Case of lysozyme crystal”,\u00a0 J. Biomolecular Structure and Dynamics, (1995), 13 (2), 219.<\/p>\n
160)\u00a0\u00a0\u00a0 Ohshima, H., Mishonova, E. and Alexov, E. Electrostatic interactions between two charged spheres, Biophysical Chemistry (1996), 57, 189- 203.<\/p>\n
161)\u00a0\u00a0\u00a0 Alexov, E. “High-frequency backward waves in longitudinally magnetized gyrotropic waveguides”, Contrib. Plasma Phys. (1995), 35, 23-32.<\/p>\n
162)\u00a0\u00a0\u00a0 Alexov, E. , Atanasov, B. and Ueki, T. “Anisotropic behavior of the pH-dependence part of Young’s modulus in a lysozyme triclinic crystal”, Biopolymers (1994), 33,513 – 522.<\/p>\n
163)\u00a0\u00a0\u00a0 Alexov, E. and Mishonova, E. “Modeling of electrostatic potential created by spherical molecule” J. Macromolecular Science: Physics (1994), B33, 21-36.<\/p>\n
164)\u00a0\u00a0\u00a0 Alexov, E. and Atanasov, B. “Analysis of electrostatic interactions in ribonuclease A monoclinic crystal” Biochimica et Biophysica Acta, (1994), 1206, 55-62.<\/p>\n
165)\u00a0\u00a0\u00a0 Alexov, E.,, Ivanov, S.T. and Kapchinskii, M.I, “Rejection band in waveguide filled with cold magnetoactive plasma”, Jpn. J. Appl. Phys. (1994),33, 5A, 2730-2734<\/p>\n
166)\u00a0\u00a0\u00a0 Ivanov S.T., Ivanova K.M. and Alexov E.G., “Polaritons along the interface between an anysotropic semiconductor and a metallic screen”, Physica Scripta, (1994), 48, 568.<\/p>\n
167)\u00a0\u00a0\u00a0 Ivanov S.T. and Alexov E.G., “Cherenkov generation of rayleigh electromagnetic wave in a gyrotropic plasma waveguide”, Nuclear Instruments & Methods in Physics Research (1994), A 341, 109.<\/p>\n
168)\u00a0\u00a0\u00a0 Ivanov S.T., Ivanova .M., Alexov E.G., ” Rayleigh surface waves along the boundary between a plasma and metallic screen”, J. Plasma Phys., (1993), 49, 227.<\/p>\n
169)\u00a0\u00a0\u00a0 Alexov E.G., Ivanov S.T., “Nonreciprocal effects in a plasma waveguide”, IEEE Trans. Plasma Sci. , (1993), 21, #2 , 254 – 257.<\/p>\n
170)\u00a0\u00a0\u00a0 Alexov E.G. , “An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma”, Phys. Scripta, (1992), 46, 429.<\/p>\n
171)\u00a0\u00a0\u00a0 Ivanov, S.T., Alexov, E. \u201cHigh-frequency electromagnetic waves in plasma waveguide\u201d, Annuaire de L\u2019Universite de Sofia (1992), 82, 113.<\/p>\n
172)\u00a0\u00a0\u00a0 Alexov E.G., Ivanov S.T., “Anysotropic HE mode in a plasma waveguide”,\u00a0 Sov. J. Plasma Phys. (USA), 1990, 16, 493.<\/p>\n
173)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., Bogdanov A.T., Malinov P.N., “Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field”, Plasma Phys. Control. Fusion, (1990), 32 , 791.<\/p>\n
174)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G. , Malinov E.G., \u201cSurface anisotropic plasma waves\u201d, Phys. Scripta, (1990), 42, 452.<\/p>\n
175)\u00a0\u00a0\u00a0 Ivanov S.T., Bogdanov A.T., Alexov E.G., “A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma”, Phys. Scripta, (1990), 42, 458.<\/p>\n
176)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., “Electromagnetic waves in a homogeneously plasma-filled\u00a0 waveguide”,\u00a0 J. Plasma Phys., (1990), 43, 51.<\/p>\n
177)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., “Cyclotron waves in a plasma-filled waveguide”, Sov. J. Plasma Phys. (USA), 1989, 15, 657.<\/p>\n
178)\u00a0\u00a0\u00a0 Ivanov S.T, Alexov E.G., “Electromagnetic waves in waveguide partially filled with semiconductor plasma”, Contrib. Plasma Phys., (1990), 30, 763.<\/p>\n
179)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., Malinov P.N., “Nonsymmetrical electromagnetic waves in partially plasma – filled waveguide”, Contrib. Plasma Phys., (1990), 30, 755.<\/p>\n
180)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., “Electromagnetic waves in the semiconductor plasma waveguide”, Phys. Scripta, (1989),40, 58.<\/p>\n
181)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., Malinov P.N., “Symmetrical electromagnetic waves in partially-filled plasma waveguide”, Plasma Phys. Control. Fusion, (1989), 31, 941.<\/p>\n
182)\u00a0\u00a0\u00a0 Alexov E.G., Ivanov S.T. “Electromagnetic waves in plasma waveguide”, Sov. J. Plasma Phys. (USA), (1988), 14, 883.<\/p>\n
183)\u00a0\u00a0\u00a0 Aleksov, E., Ivanov, S.T., Shvachka, A.B. \u201cNumerical analysis of the electromagnetic wave dispersion in the waveguide filled with semiconductor plasma. Magnetoactive plasma\u201d, Comm. of the Joint Institute for Nuclear Research, Dubna (1984), P11-84-766.<\/p>\n
184)\u00a0\u00a0\u00a0 Aleksov, E., Ivanov, S.T., Shvachka, A.B. \u201cNumerical analysis of the electromagnetic wave dispersion in the waveguide filled with semiconductor plasma. Unmagnetized and magnetized plasma\u201d, Comm. of the Joint Institute for Nuclear Research, Dubna (1984), P11-84-592<\/p>\n
<\/p>\n
Last update 3 May 2022<\/p>\n
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[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"
Professor, Department of Physics and Astronomy Email: ealexov@g.clemson.edu Bioshetch Emil Alexov is a professor of biophysics and bioinformatics in the Department of Physics and Astronomy. He is also Edior-in-Chief of the Journal of Computational Biophysics and Chemistry, and editor for Genes, PLOS Computational Biology and many others. Currently his lab is maintaining and developing DelPhi […]<\/p>\n","protected":false},"author":32,"featured_media":1275,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"Professor, Department of Physics and Astronomy\r\n\r\nEmail: ealexov@g.clemson.edu\r\n\r\n\r\n\r\n \r\n\r\nBioshetch<\/strong>\r\n\r\nEmil Alexov is a professor of biophysics and bioinformatics in the Department of Physics and Astronomy. He is also Edior-in-Chief of the Journal of Computational Biophysics and Chemistry, and editor for Genes, PLOS Computational Biology and many others. Currently his lab is maintaining and developing DelPhi package for modeling electrostatics in proteins, RNAs and DNAs. Furthermore, his lab developed numerous tools for predicting effect of mutations on protein stability and binding, including protein-DNA binding.\r\n\r\nResearch<\/strong>\r\n\r\nDr. Alexov is working to advance personalized medicine and the understanding of molecular mechanisms of human disease in order to more effectively prevent diseases before they even happen.\u00a0 He and his research team look for how DNA variants and other factors cause diseases and identify small molecules (plausible drugs) that bind to dysfunctional mutant protein and restore the wild type function.\r\n\r\nPublications<\/strong>\r\n\r\n1)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 SK Panday, E Alexov,\u00a0 Protein\u2013Protein Binding Free Energy Predictions with the MM\/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation, ACS omega, 2022\r\n\r\n2)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 G Li, SK Panday, Y Peng, E Alexov, SAMPDI-3D: predicting the effects of protein and DNA mutations on protein\u2013DNA interactions, Bioinformatics 37 (21), 3760-3765, 2021\r\n\r\n3)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 R Aprigliano, ME Aksu, S Bradamante, B Mihaljevic, W Wang, K Rian, Increased p53 signaling impairs neural differentiation in HUWE1-promoted intellectual disabilities, ...Cell Reports Medicine 2 (4), 100240, 3,\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 2021\r\n\r\n4)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 G Li, S Pahari, AK Murthy, S Liang, R Fragoza, H Yu, E Alexov, SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein\u2013protein binding affinity, Bioinformatics 37 (7), 992-999, 10\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 2021\r\n\r\n5)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Y Peng, R Kelle, C Little, E Michonova, KG Kornev, E Alexov, pH-dependent interactions of Apolipophorin-III with a lipid disk, Journal of Computational Biophysics and Chemistry 20 (02), 153-164,\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 3, 2021\r\n\r\n6)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 E Alexov, Special Issue on Computational Chemistry Methods to Predict pKa\u2019s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules, Journal of Computational Biophysics and Chemistry 20 (02), 109-110, 2021\r\n\r\n7)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 E Alexov, Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry, Journal of Computational Biophysics and Chemistry 20 (01), 1-1\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 , 2021\r\n\r\n8)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 B Wu, W Hand, E Alexov, Opioid addiction and opioid receptor dimerization: structural modeling of the OPRD1 and OPRM1 heterodimer and its signaling pathways, International journal of molecular sciences 22 (19), 10290, 1, 2021\r\n\r\n9)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, HB Shashikala, J Jeffries, B Wu, SK Loftus, JH Zippin, E Alexov, Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease, International journal of molecular sciences 22 (15), 8273, \u00a0\u00a0\u00a0\u00a0 2021\r\n\r\n10)\u00a0\u00a0\u00a0\u00a0\u00a0 S Wang, E Alexov, S Zhao, On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary, Mathematical Biosciences and Engineering 18 (2)\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 3, 2021\r\n\r\n11)\u00a0\u00a0\u00a0\u00a0\u00a0 G Li, SK Panday, E Alexov, SAAFEC-SEQ: a sequence-based method for predicting the effect of single point mutations on protein thermodynamic stability, International journal of molecular sciences 22 (2), 606, 18, 2021\r\n\r\n12)\u00a0\u00a0\u00a0\u00a0\u00a0 HBM Shashikala, A Chakravorty, SK Panday, E Alexov, BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics, International Journal of Molecular Sciences 22 (1), 272, \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 1, 2020\r\n\r\n13)\u00a0\u00a0\u00a0\u00a0\u00a0 SR Ganakammal, M Koirala, B Wu, E Alexov, In-silico analysis to identify the role of MEN1 missense mutations in breast cancer, Journal of Theoretical and Computational Chemistry 19 (06), 2041002, 3\u00a0\u00a0\u00a0\u00a0\u00a0 2020\r\n\r\n14)\u00a0\u00a0\u00a0\u00a0\u00a0 E Alexov, An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants. Genes 11 (9), 2020\r\n\r\n15)\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, E Alexov, Computational chemistry methods to investigate the effects caused by DNA variants linked with disease, Journal of Theoretical and Computational Chemistry 19 (06), 1930001, 1, 2020\r\n\r\n16)\u00a0\u00a0\u00a0\u00a0\u00a0 S Ranganathan Ganakammal, E Alexov, An ensemble approach to predict the pathogenicity of synonymous variants, Genes 11 (9), 1102, 4, 2020\r\n\r\n17)\u00a0\u00a0\u00a0\u00a0\u00a0 YR Lee, K Khan, K Armfield-Uhas, S Srikanth, NA Thompson, M Pardo, Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy, ...Nature communications 11 (1), 1-17, 17, 2020\r\n\r\n18)\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, E Alexov, Ab-initio binding of barnase\u2013barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach, Journal of Theoretical and Computational Chemistry 19 (04), 2050016.\r\n\r\n19)\u00a0\u00a0\u00a0\u00a0\u00a0 C Li, M McGowan, E Alexov, S Zhao, A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation, Mathematical Biosciences and Engineering 17 (6).\r\n\r\n20)\u00a0\u00a0\u00a0\u00a0\u00a0 S Wang, A Lee, E Alexov, S Zhao. A regularization approach for solving Poisson\u2019s equation with singular charge sources and diffuse interfaces. Applied Mathematics Letters 102, 106144\r\n\r\n21)\u00a0\u00a0\u00a0\u00a0\u00a0 A Chakravorty, S Panday, S Pahari, S Zhao, E Alexov. Capturing the effects of explicit waters in implicit electrostatics modeling: Qualitative justification of Gaussian-based dielectric models in DelPhi. Journal of Chemical Information and Modeling\r\n\r\n22)\u00a0\u00a0\u00a0\u00a0\u00a0 S Pahari, G Li, AK Murthy, S Liang, R Fragoza, H Yu, E Alexov. SAAMBE-3D: Predicting Effect of Mutations on Protein\u2013Protein Interactions. International journal of molecular sciences 21 (7), 2563\r\n\r\n23)\u00a0\u00a0\u00a0\u00a0\u00a0 SR Ganakammal, E Alexov. Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: application to Rett syndrome variants. PeerJ 7, e8106\r\n\r\n24)\u00a0\u00a0\u00a0\u00a0\u00a0 SK Panday, MHB Shashikala, M Koirala, S Pahari, A Chakrvorty, Y Peng, ...E. Alexov. Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]. Living Journal of Computational Molecular Science 1 (2), 10841C\r\n\r\n25)\u00a0\u00a0\u00a0\u00a0\u00a0 Li, Z Jia, A Chakravorty, S Pahari, Y Peng, S Basu, M Koirala, \u2026 E. Alexov. DelPhi Suite: New Developments and Review of Functionalities. Journal of Computational Chemistry 40 (28), 2502-2508\r\n\r\n26)\u00a0\u00a0\u00a0\u00a0\u00a0 M Koirala, E Alexov. Computational chemistry methods to investigate the effects caused by DNA variants linked with disease. Journal of Theoretical and Computational Chemistry, 1930001.\r\n\r\n27)\u00a0\u00a0\u00a0\u00a0\u00a0 T Hazra, SA Ullah, S Wang, E Alexov, S Zhao. A super-Gaussian Poisson\u2013Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.\u00a0 Journal of mathematical biology 79 (2), 631-672\r\n\r\n28)\u00a0\u00a0\u00a0\u00a0\u00a0 N Tajielyato, E Alexov. Modeling pKas of unfolded proteins to probe structural models of unfolded state.\u00a0 Journal of Theoretical and Computational Chemistry 18 (04), 1950020\r\n\r\n29)\u00a0\u00a0\u00a0\u00a0\u00a0 Spellicy CJ, Peng Y, Olewiler L, Cathey SS, Rogers RC, Bartholomew D, Johnson J, Alexov E, Lee JA, Friez MJ, Jones JR. Three additional patients with EED-associated overgrowth: potential mutation hotspots identified? J Hum Genet. 2019 Mar 11. doi: 10.1038\/s10038-019-0585-5.\r\n\r\n30)\u00a0\u00a0\u00a0\u00a0\u00a0 Tajielyato N, Alexov E. Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. Int J Mol Sci. 2019 Mar 3;20(5). pii: E1090. doi: 10.3390\/ijms20051090.\r\n\r\n31)\u00a0\u00a0\u00a0\u00a0\u00a0 Pahari S, Sun L, Alexov E. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database (Oxford). 2019 Jan 1;2019. pii: baz024. doi: 10.1093\/database\/baz024.\r\n\r\n32)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Gallicchio E, Alexov E. A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. J Comput Chem. 2019 May 5;40(12):1290-1304. doi: 10.1002\/jcc.25786. Epub 2019 Jan 30.\r\n\r\n33)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci. 2019 Jan 28;20(3). pii: E548. doi: 10.3390\/ijms20030548.\r\n\r\n34)\u00a0\u00a0\u00a0\u00a0\u00a0 Pahari S, Sun L, Basu S, Alexov E. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins. 2018 Dec;86(12):1277-1283. doi: 10.1002\/prot.25608. Epub 2018 Oct 26\r\n\r\n35)\u00a0\u00a0\u00a0\u00a0\u00a0 Tajielyato N, Li L, Peng Y, Alper J, Alexov E. E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein. Sci Rep. 2018 Sep 5;8(1):13266. doi: 10.1038\/s41598-018-31480-9.\r\n\r\n36)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Jia Z, Peng Y, Tajielyato N, Wang L, Alexov E. Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents. Front Mol Biosci. 2018 Mar 27;5:25. doi: 10.3389\/fmolb.2018.00025\r\n\r\n37)\u00a0\u00a0\u00a0\u00a0\u00a0 Spellicy CJ, Norris J, Bend R, Bupp C, Mester P, Reynolds T, Dean J, Peng Y, Alexov E, Schwartz CE, Stevenson RS, J Friez M. Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects. Eur J Hum Genet. 2018 Mar;26(3):420-427.\r\n\r\n38)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Jia Z, Li L, Zhao S, Alexov E. Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling. J Chem Theory Comput. 2018 Feb 13;14(2):1020-1032. doi: 10.1021\/acs.jctc.7b00756. Epub 2018 Feb 3.\r\n\r\n39)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Myers R, Zhang W, Alexov E. Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome. Int J Mol Sci. 2018 Jan 4;19(1). pii: E141. doi: 10.3390\/ijms19010141.\r\n\r\n40)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Sun L, Jia Z, Li L, Alexov E. Predicting protein-DNA binding free energy change upon missense mutations using modified MM\/PBSA approach: SAMPDI webserver. Bioinformatics. 2018 Mar 1;34(5):779-786. doi: 10.1093\/bioinformatics\/btx698.\r\n\r\n41)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E. DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinformatics. 2017 Nov 15;33(22):3661-3663. doi: 10.1093\/bioinformatics\/btx495\r\n\r\n42)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Jia Z, Peng Y, Godar S, Getov I, Teng S, Alper J, Alexov E. Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. Sci Rep. 2017 Aug 15;7(1):8237. doi: 10.1038\/s41598-017-08419-7.\r\n\r\n43)\u00a0\u00a0\u00a0\u00a0\u00a0 Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem. 2017 Aug 15;38(22):1974-1979. doi: 10.1002\/jcc.24831.\r\n\r\n44)\u00a0\u00a0\u00a0\u00a0\u00a0 Hoffman L, Li L, Alexov E, Sanabria H, Waxham MN. Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner. Biochemistry. 2017 Mar 24. doi: 10.1021\/acs.biochem.7b00028\r\n\r\n45)\u00a0\u00a0\u00a0\u00a0\u00a0 Vaidyanathan K, Niranjan T, Selvan N, Teo CF, May M, Patel S, Weatherly B, Skinner C, Opitz J, Carey J, Viskochil D, Gecz J, Shaw M, Peng Y, Alexov E, Wang T, Schwartz C, Wells L. Identification and Characterization of a Missense Mutation in the O-GlcNAc Transferase Gene that Segregates with X-Linked Intellectual Disability. J Biol Chem. 2017 Mar 16. pii: jbc.M116.771030. doi: 10.1074\/jbc.M116.771030\r\n\r\n46)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakravorty A, Jia Z, Li L, Alexov E. A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential. Langmuir. 2017 Feb 20. doi: 10.1021\/acs.langmuir.6b04430. [Epub ahead of print]. PMID: 28181811\r\n\r\n47)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Chakravorty A, Alexov E. DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem. 2017 Apr 5;38(9):584-593. doi: 10.1002\/jcc.24715. PMID: 28130775\r\n\r\n48)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E. Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes. Proteins. 2017 Feb;85(2):282-295. doi: 10.1002\/prot.25221. PMID: 27936518\r\n\r\n49)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E. Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. Proteins. 2016 Dec;84(12):1797-1809. doi: 10.1002\/prot.25162. PMID: 27696497\r\n\r\n50)\u00a0\u00a0\u00a0\u00a0\u00a0 Chakavorty A, Li L, Alexov E. Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. J Comput Chem. 2016 Aug 21. doi: 10.1002\/jcc.24475. PMID: 27546093\r\n\r\n51)\u00a0\u00a0\u00a0\u00a0\u00a0 Yang Y, Kucukkal TG, Li J, Alexov E, Cao W. Binding Analysis of Methyl-CpG Binding Domain of MeCP2 and Rett Syndrome Mutations. ACS Chem Biol. 2016 Oct 21;11(10):2706-2715. Epub 2016 Aug 8. PMID: 27356039\r\n\r\n52)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Dai L, Alexov E. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations. Int J Mol Sci. 2016 Apr 12;17(4). pii: E547. doi: 10.3390\/ijms17040547. PMID: 27077847\r\n\r\n53)\u00a0\u00a0\u00a0\u00a0\u00a0 Getov I, Petukh M, Alexov E. SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM\/PBSA Approach.\u00a0 Int J Mol Sci. 2016 Apr 7;17(4). pii: E512. doi: 10.3390\/ijms17040512. PMID: 27070572\r\n\r\n54)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Alper J, Alexov E. Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Sci Rep. 2016 Mar 18;6:23249. doi: 10.1038\/srep23249. PMID:\u00a0 26988596\r\n\r\n55)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Norris J, Schwartz C, Alexov E. Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase. Int J Mol Sci. 2016 Jan 8;17(1). pii: E77. doi: 10.3390\/ijms17010077. PMID:\u00a0 26761001\r\n\r\n56)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Alexov E., Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. Proteins. 2015 Dec 9. doi: 10.1002\/prot.24968. [Epub ahead of print], PMID: 26650512\r\n\r\n57)\u00a0\u00a0\u00a0\u00a0\u00a0 Peng Y, Suryadi J, Yang Y, Kucukkal TG, Cao W, Alexov E., Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease, Int J Mol Sci. 2015 Nov 13;16(11):27270-87. doi: 10.3390\/ijms161126022.\r\n\r\n58)\u00a0\u00a0\u00a0\u00a0\u00a0 Wang L, Zhang M, Alexov E., DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs, Bioinformatics. 2015 Oct 29. pii: btv607.\r\n\r\n59)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Zhang M, Alexov E., Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence, J Comput Chem. 2015 Oct 20. doi: 10.1002\/jcc.24218.\r\n\r\n60)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Yang Y, Uvarov O, Cao W, Alexov E., Impact of Rett Syndrome Mutations on MeCP2 MBD Stability, Biochemistry. 2015 Oct 20;54(41):6357-68. doi: 10.1021.\r\n\r\n61)\u00a0\u00a0\u00a0\u00a0\u00a0 Wang L, Li L, Alexov E., pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa, Proteins. 2015 Sep 26. doi: 10.1002\/prot.24935.\r\n\r\n62)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Li M, Alexov E, Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM\/PBSA Method, PLoS Comput Biol. 2015 Jul 6;11(7):e1004276. doi: 10.1371.\r\n\r\n63)\u00a0\u00a0\u00a0\u00a0\u00a0 Emil Alexov \u201cAdvances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine, Advances in Biology 2015, ID 471836\r\n\r\n64)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Alexov E., Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2, Comput Math Methods Med. 2015;2015:746157. doi: 10.1155\r\n\r\n65)\u00a0\u00a0\u00a0\u00a0\u00a0 May M, Hwang KS, Miles J, Williams C, Niranjan T, Kahler SG, Chiurazzi P, Steindl K, Van Der Spek PJ, Swagemakers S, Mueller J, Stefl S, Alexov E, Ryu JI, Choi JH, Kim HT, Tarpey P, Neri G, Holloway L, Skinner C, Stevenson RE, Dorsky RI, Wang T, Schwartz CE, Kim CH, ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons, Hum Mol Genet. 2015 Sep 1;24(17):4848-61. doi: 10.1093.\r\n\r\n66)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Wang L, Alexov E., On the energy components governing molecular recognition in the framework of continuum approaches, Front Mol Biosci. 2015 Mar 6;2:5. doi: 10.3389\r\n\r\n67)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Alexov E., Ion binding to biological macromolecules, Asian J Phys. 2014 Nov;23(5):735-744.\r\n\r\n68)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Kucukkal TG, Alexov E., On human disease-causing amino acid variants: statistical study of sequence and structural patterns, Hum Mutat. 2015 May;36(5):524-34. doi: 10.1002\r\n\r\n69)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Petukh M, Li L, Alexov E., Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins, Curr Opin Struct Biol. 2015 Jun;32:18-24. doi: 10.1016.\r\n\r\n70)\u00a0\u00a0\u00a0\u00a0\u00a0 Campbell B, Petukh M, Alexov E, Li C., On the electrostatic properties of homodimeric proteins, J Theor Comput Chem. 2014;13(3).\r\n\r\n71)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Wu B, Stefl S, Smith N, Hyde-Volpe D, Wang L, Alexov E., Chronic Beryllium Disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2, PLoS One. 2014 Nov 4;9(11):e111604.\r\n\r\n72)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Martiny V, Lagorce D, Ikeguchi Y, Alexov E, Miteva MA., Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach, PLoS One. 2014 Oct 23;9(10):e110884.\r\n\r\n73)\u00a0\u00a0\u00a0\u00a0\u00a0 Kimmett T, Smith N, Witham S, Petukh M, Sarkar S, Alexov E., ProBLM web server: protein and membrane placement and orientation package, Comput Math Methods Med. 2014;2014:838259.\r\n\r\n74)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Li C, Alexov E., On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function, J Theor Comput Chem. 2014 May;13(3).\r\n\r\n75)\u00a0\u00a0\u00a0\u00a0\u00a0 Kucukkal TG, Yang Y, Chapman SC, Cao W, Alexov E., Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics, Int J Mol Sci. 2014 May 30;15(6):9670-717\r\n\r\n76)\u00a0\u00a0\u00a0\u00a0\u00a0 Li M, Petukh M, Alexov E, Panchenko AR., Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity, J Chem Theory Comput. 2014 Apr 8;10(4):1770-1780\r\n\r\n77)\u00a0\u00a0\u00a0\u00a0\u00a0 Dias RP, Li L, Soares TA, Alexov E., Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi, J Comput Chem. 2014 Jul 15;35(19):1418-29.\r\n\r\n78)\u00a0\u00a0\u00a0\u00a0\u00a0 Nedumpully-Govindan P, Li L, Alexov EG, Blenner MA, Ding F., Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity, Bioinformatics. 2014 Aug 15;30(16):2302-9.\r\n\r\n79)\u00a0\u00a0\u00a0\u00a0\u00a0 Alexov E, Sternberg M., Understanding molecular effects of naturally occurring genetic differences, J Mol Biol. 2013 Nov 1;425(21):3911-3.\r\n\r\n80)\u00a0\u00a0\u00a0\u00a0\u00a0 Onufriev AV, Alexov E., Protonation and pK changes in protein-ligand binding. Q Rev Biophys. 2013 May;46(2):181-209.\r\n\r\n81)\u00a0\u00a0\u00a0\u00a0\u00a0 Boccuto L, Aoki K, Flanagan-Steet H, Chen CF, Fan X, Bartel F, Petukh M, Pittman A, Saul R, Chaubey A, Alexov E, Tiemeyer M, Steet R, Schwartz CE. \u201cA mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation\u201d, Hum Mol Genet. 2013 Sep 26.\r\n\r\n82)\u00a0\u00a0\u00a0\u00a0\u00a0 Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E \u201cMolecular Mechanisms of Disease-Causing Missense Mutations\u201d, J Mol Biol. 2013 Jul 16. doi:pii: S0022-2836(13)00446-4. 10.1016\/j.jmb.2013.07.014. [Epub ahead of print]\r\n\r\n83)\u00a0\u00a0\u00a0\u00a0\u00a0 Dolzhanskaya N, Gonzalez M, Stefl S, Messing J, Wen GY, Alexov E, Zuchner S, Velinov M \u201cA novel Leu(381)Phe mutation in Presenilin 1 is associated with very early onset and unusually fast progressing dementia, and lysosomal inclusions typically seen in Kufs disease\u201d, Journal of Alzheimer's Disease, 2014;39(1):23-7. doi: 10.3233\r\n\r\n84)\u00a0\u00a0\u00a0\u00a0\u00a0 Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR. \u201cCancer missense mutations alter binding properties of proteins and their interaction networks\u201d, PLoS One. 2013 Jun 14;8(6):e66273.\r\n\r\n85)\u00a0\u00a0\u00a0\u00a0\u00a0 Li C, Petukh M, Li L, Alexov E. \u201cContinuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi\u201d, J Comput Chem. 2013 Jun 4. doi: 10.1002\/jcc.23340.\r\n\r\n86)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Norris J, Kalscheuer V, Wood T, Wang L, Schwartz C, Alexov E, Van Esch H. \u201cA Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome\u201d, Hum Mol Genet. 2013 May 31.\r\n\r\n87)\u00a0\u00a0\u00a0\u00a0\u00a0 Chuan Li, Lin Li, Marharyta Petukh and Emil Alexov; \"Progress in developing Poisson-Boltzmann equation solvers\"; Molecular Based Mathematical Biology. 2013, Volume 1, Pages 42-62.\r\n\r\n88)\u00a0\u00a0\u00a0\u00a0\u00a0 Li L, Li C, Zhang Z, Alexov E.; \"On the Dielectric \"Constant\" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi\"; J Chem Theory Comput. 2013 Apr 9;9(4):2126-2136.\r\n\r\n89)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E. \"Enhancing human spermine synthase activity by engineered mutations.\" PLoS Comput Biol. 2013 Feb;9(2):e1002924. doi:10.1371\/journal.pcbi.1002924. Epub 2013 Feb 28. Figure 2 of the manuscript is taken for the cover page of the journal\r\n\r\n90)\u00a0\u00a0\u00a0\u00a0\u00a0 Zhang Z, Witham S, Petukh M, Moroy G, Miteva M, Ikeguchi Y, Alexov E. \"A rational free energy-based approach to understanding and targeting disease-causing missense mutations.\" J Am Med Inform Assoc. 2013 Feb 13. [Epub ahead of print]\r\n\r\n91)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Kimmet T, Alexov E. \"BION web server: predicting non-specifically bound surface ions.\" Bioinformatics. 2013 Mar 15;29(6):805-6\r\n\r\n92)\u00a0\u00a0\u00a0\u00a0\u00a0 Smith N, Campbell B, Li L, Li C, Alexov E. \"Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.\" BMC Struct Biol. 2012 Dec 5;12:31. doi:10.1186\/1472-6807-12-31.\r\n\r\n93)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Stefl S, Alexov E \"The Role of Protonation States in Ligand Receptor Recognition and Binding.\" Curr Pharm Des. 2012 Nov 20. [Epub ahead of print]\r\n\r\n94)\u00a0\u00a0\u00a0\u00a0\u00a0 Takano K, Lieu D, Tarpey P, Gallant E, Lam A, Witham S, Alexov E, Chaubey A, Stevenson RE, Schwartz CE, Board PG, Dulhunty AF \"An X-linked Channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity\", Hum Mol Genet. 2012 Aug Oct 15;21(20):4497-507. Epub 2012 Jul 19.\r\n\r\n95)\u00a0\u00a0\u00a0\u00a0\u00a0 Petukh M, Zhenirovskyy M, Li C, Li L, Wang L, Alexov E. \"Predicting nonspecific ion binding using Delphi\", Biophys J. 2012 Jun 20, 102(12)\r\n\r\n96)\u00a0\u00a0\u00a0\u00a0\u00a0 Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia and Emil Alexov \"DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes\", Comm. Comp. Phys., (2013), 13, 269-84\r\n\r\n97)\u00a0\u00a0\u00a0\u00a0\u00a0 Lin Wang, Shawn Witham, Zhe Zhang, Lin Li, Michael Hodsdon and Emil Alexov \"In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor\", Comm. Comp. Phys., (2013), 13, 207-222\r\n\r\n98)\u00a0\u00a0\u00a0\u00a0\u00a0 Lin Wang, Zhe Zhang, Walter Rocchia and Emil Alexov \"Using DelPhi capabilities to mimic protein\u2019s conformational reorganization with amino acid specific dielectric constants\", Comm. Comp. Phys., (2013), 13, 13-30\r\n\r\n99)\u00a0\u00a0\u00a0\u00a0\u00a0 Sergio Decherchi, Jos\u00b4e Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, and Walter Rocchia \"Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution\", Comm. Comp. Phys., (2013), 13, 61-89\r\n\r\n100)\u00a0\u00a0\u00a0 Li C, Li L, Zhang J, Alexov E., \"Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi.\", J Comput Chem. 2012 Sep 15;33(24):1960-6. doi: 10.1002\/jcc.23033. Epub 2012 Jun 4.; Figure 3 of the manuscript is the cover page of the journal: J Comput Chem. 2012 Sep 15;33(24):iii-iv. doi:10.1002\/jcc.22080\r\n\r\n101)\u00a0\u00a0\u00a0 Zhe Zhang, Maria A. Miteva, Lin Wang and Emil Alexov \"Analyzing Effects of Naturally Occurring Missense Mutations\" Computational and Mathematical Methods in Medicine, Volume 2012 (2012), Article ID 805827, doi:10.1155\/2012\/805827\r\n\r\n102)\u00a0\u00a0\u00a0 Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z, Wang L, Smith N, Petukh M, Alexov E. \"DelPhi: a comprehensive suite for DelPhi software and associated resources.\" BMC, Biophys, (2012) May14;4(1):9.\r\n\r\n103)\u00a0\u00a0\u00a0 Nicholas Smith, Subhra Sarkar, Shawn Witham, Jie Zhang, Lin Li, Chuan Li and Emil Alexov \"DelPhi Web Server v2: Incorporating atomic-style geometrical figures into the computational protocol\", Bioinformatics (2012), 28(12):1655-7.\r\n\r\n104)\u00a0\u00a0\u00a0 Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E, \"Predicting folding free energy changes upon single point mutations\", Bioinformatics, (2012), 28(5):664-71.\r\n\r\n105)\u00a0\u00a0\u00a0 Mitra, R., Zhang. Zhe and Alexov, E, \"In silico modeling of pH-optimum of protein-protein binding\", Proteins (2011), 171, 285-289.\r\n\r\n106)\u00a0\u00a0\u00a0 Zhang, Zhe, Witham, S. and Alexov, E., \"On the role of electrostatics on protein-protein interactions\", Physical Biology 2011 Jun;8(3):035001. Epub 2011 May 13.\r\n\r\n107)\u00a0\u00a0\u00a0 Zhang, Zhe, Norris, J., Schwartz, C. and Alexov, E. \"In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in Spermine Synthase\", PLoS One, (2011);6(5):e20373.\r\n\r\n108)\u00a0\u00a0\u00a0 Witham, S., Takano, K., Schwartz, C. and Alexov, E. \"A Missense Mutation in CLIC2 Associated with Intellectual Disability is Predicted by In Silico Modeling to Affect Protein Stability and Dynamics\", Proteins, (2011) 79(8):2444-54. doi: 10.1002\/prot.23065.\r\n\r\n109)\u00a0\u00a0\u00a0 Alexov, E., Mehler, E.L., Baker, N., Baptista, A.M., Huang, Y., Milletti, F., Nielsen, J.E., Farrell, D., Carstensen, T., Olsson, M.H.M., Shen, J.K., Warwicker, J., Williams, S., and Word, J.M., \"Progress in the prediction of pKa values in proteins\", Proteins, (2011), 79(12):3260-75, doi:10.1002\/prot.23189.\r\n\r\n110)\u00a0\u00a0\u00a0 Teng S, Srivastava AK, Schwartz CE, Alexov E, Wang L , \u201cStructural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interactions\u201d, Int J Comput Biol Drug Des. 2011;3(4):334-49.\r\n\r\n111)\u00a0\u00a0\u00a0 Mitra, R., Zhang. Zhe and Alexov, E, \u201cIn silico modeling of pH-optimum of protein\u2013protein binding\u201d, Proteins (2011), 171, 285-289.\r\n\r\n112)\u00a0\u00a0\u00a0 Talley, K. and Alexov, E. \u201cOn the pH-optimum of activity and stability\u201d, Proteins (2010), 78, 2699-706.\r\n\r\n113)\u00a0\u00a0\u00a0 Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E. \u201cComputational analysis of missense mutations causing Snyder-Robinson syndrome\u201d, Hum Mutat. (2010) 31(9):1043-9.\r\n\r\n114)\u00a0\u00a0\u00a0 Mitra, R. and Alexov, E.\u00a0 \u201cAnalyzing and Predicting Protein Binding Pockets In Silico Lead Discovery, 2011, 84-98.\r\n\r\n115)\u00a0\u00a0\u00a0 Teng, S., Madej, T., Panchenko, A. and Alexov, E. \u201cModeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions\u201d, Biophysical Journal, (2009), 96, 2178-2188.\r\n\r\n116)\u00a0\u00a0\u00a0 Talley Kemper, Ng Carmen, Snoppell Michael, Kundrotas Petras and Alexov E.\u00a0 \"On the electrostatic component of protein-protein binding free energy\u201d\u00a0 PMC Biophysics 2008,1:2\u00a0 1-23.\r\n\r\n117)\u00a0\u00a0\u00a0 Kosloff M., Alexov E., Arshavsky Y. and Hong B. \"Electrostatic and Lipid Anchor Contributions to the Interaction of Transduin with Membrane\u201d\u00a0 The Journal of Biological Chemistry 283(2008)\u00a0 31197-31207.\r\n\r\n118)\u00a0\u00a0\u00a0 Mitra, R, Shyam, R., Mitra, I., Miteva, M. and Alexov, E \u201cCalculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions\u201d Current Computer-Aided Drug Design: 4: 169-179.\r\n\r\n119)\u00a0\u00a0\u00a0 Kundrotas, P, Lensink, M. and Alexov, E. \u201cHomology-based modeling of 3D structures of protein-protein complexes using alignment of modified sequence profiles\u201d, Int. J. Biol. Macromol. (2008), 43: 198-208.\r\n\r\n120)\u00a0\u00a0\u00a0 Alexov, E.\u00a0 \u201c Editorial\u201d,\u00a0\u00a0 Current Pharmaceutical Biotechnology (2008) 9:55-56.\r\n\r\n121)\u00a0\u00a0\u00a0 Miteva, A.Maria, Alexov , Emil, Villoutreix, Bruno.O\u00a0 \"Protein Structure Analysis Online\u201d\u00a0 Current Protocols in Protein Science (2007)\u00a0 2:13:1-23.\r\n\r\n122)\u00a0\u00a0\u00a0 Teng S., Michonova-Alexova E and Alexov, E.\u00a0 \"Approaches and Resources for prediction of the Effects of Non-Synonymous Single Nucleotide Polymorphism on Protein Function and Intearctions\u201d\u00a0 Current Pharmaceutical Biotechnology (2008) 9:123-133.\r\n\r\n123)\u00a0\u00a0\u00a0 Talley, K., Kundrotas, P. and Alexov, E. \u201cModeling Salt Dependence of Protein-Protein Association: Linear vs Non-Linear Poisson-Boltzmann Equation\u201d. Comm. Comp. Phys. (2008), 3: 1071.\r\n\r\n124)\u00a0\u00a0\u00a0 Kundrotas P. and Alexov E. \u201cPredicting interacting and interfacial residues using continuous sequence segments\u201d Int J Biol Macromol. 2007 Dec 1;41(5):615-23. Epub 2007 Aug 9.\r\n\r\n125)\u00a0\u00a0\u00a0 Brook K., Talley. K., Coley. K., Kundrotas P., Alexov. E. \u201cOptimization of electrostatic interactions in protein-protein complexes\u201d. Biophys J. 2007 Nov 15;93(10):3340-52. Epub 2007 Aug 10.\r\n\r\n126)\u00a0\u00a0\u00a0 Augustin Ofiretu, Nadia Bucurenci, Emil Alexov, Thomas Bertrand, Pierre Briozzo, Helene Munier-Lehmann and Anne-Marie Gilles \u201cStructural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase\u201d, FEBS Letters (2007) 274, 3363\u20133373.\r\n\r\n127)\u00a0\u00a0\u00a0 Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. \u201cAssessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families \u201d J. Bioinformatics and Comp. Biol.\u00a0 (2007), 5, 693-715.\r\n\r\n128)\u00a0\u00a0\u00a0 Kundrotas, P., Georgieva, P., Shosheva, A., Christova, P. and Alexov, E. \u201cBANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families\u201d, Int. J. Biol. Macromol.(2007), Jun 1;41(1):114-9.\r\n\r\n129)\u00a0\u00a0\u00a0 C. L. Tang, E. Alexov, A. Pyle and B. Honig \u201cCalculation of pKas in RNA: On the structural origins and functional roles of protonated nucleotides\u201d, J. Mol. Biol. (2007), Mar 9; 366(5):1475-96.\r\n\r\n130)\u00a0\u00a0\u00a0 Claudia, B., Honig, B. and Alexov, E. \u201cPoisson-Boltzmann calculations of non-specific salt effects on protein-protein binding free energies\u201d, Biophys. J. (2007), Mar 15; 92(6):1891-9.\r\n\r\n131)\u00a0\u00a0\u00a0 Isvoran, A., Craescu, C. and Alexov, E. \u201cElectrostatic control of the overall shape of calmodulin: numerical calculations\u201d Eur. Biophys. J (2007) Mar; 36(3):225-37.\r\n\r\n132)\u00a0\u00a0\u00a0 Kundrotas, P.J. and\u00a0 Alexov, E. \u201cPredicting residue contacts using pragmatic correlated mutations method: reducing the false positives\u201d BMC Bioinformatics, 2006. 7(1): p. 503.\r\n\r\n133)\u00a0\u00a0\u00a0 Kundrotas, P. and Alexov, E \u201cProtCom: Searchable database of protein-protein complexes\u201d Nuclear Acids Research (2007) 35. D575-D579.\r\n\r\n134)\u00a0\u00a0\u00a0 Kundrotas, P. and Alexov, E \u201cPredicting 3D structures of transient protein-protein complexes by homology\u201d Biochimica at Biophysica Acta\u00a0 (2006), 1764, 1498-1511.\r\n\r\n135)\u00a0\u00a0\u00a0 Kundrotas, P. and Alexov, E \u201cElectrostatic properties of protein-protein complexes\u201d Biophys. J. (2006), 91, 1724-1736.\r\n\r\n136)\u00a0\u00a0\u00a0 Wu Y, Hudson JS, Lu Q, Moore JM, Mount AS, Rao AM, Alexov E, Ke PC. \u201cCoating single-walled carbon nanotubes with phospholipids\u201d,\u00a0 J Phys Chem B (2006), 110(6):2475-2478.\r\n\r\n137)\u00a0\u00a0\u00a0 Grey MJ, Tang Y, Alexov E, McKnight CJ, Raleigh DP, Palmer AG 3rd. \u201cCharacterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain\u201d J Mol Biol (2006) 355:1078-1094.\r\n\r\n138)\u00a0\u00a0\u00a0 Shosheva, A., Donchev, A., Dimitrov, M., Kostov, G., Toromanov, G., Getov, V and E. Alexov \u201cComparative study of the stability of poplar plastocyanin isoforms\u201d Biochimica et Biophysica Acta (2005), 1748, 116-127\r\n\r\n139)\u00a0\u00a0\u00a0 Zhu, J., Alexov, E. and B. Honig \u201cComparative Study of Generalized Born Models: Born Radii and Peptide Folding\u201d J. Phys. Chem. B (2005) 109, 3008-3022.\r\n\r\n140)\u00a0\u00a0\u00a0 Alexov, E. \u201cCalculating Proton Uptake\/Release and Binding Free Energy Taking into Account Ionization and Conformation Changes Induced by Protein-Inhibitor Association: Application to Plasmepsin, Cathepsin D and Endothiapepsin-Pepstatin complexes\u201d Proteins (2004), 56, 572-584.\r\n\r\n141)\u00a0\u00a0\u00a0 Tang C., Xie L., Koh I., Posy S., Alexov E. and Honig B. \u201cOn the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles\u201d J. Mol. Biol. (2003), 334, 1043-1062.\r\n\r\n142)\u00a0\u00a0\u00a0 Shosheva, A., Donchev, A., Dimitrov, M., Zlatanav, I., Toromanov, G., Getov, V. and Alexov, E. \u201cExperimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity\u201d Biochemica at Biophysica Acta\u00a0 (2004), 1698, 67-75.\r\n\r\n143)\u00a0\u00a0\u00a0 Alexov, E. \u201cNumerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure\u201d Eur. J. Biochem. (2004), 271, 173-185.\r\n\r\n144)\u00a0\u00a0\u00a0 Petrey D., Xiang Z., Tang C., Xie. L., Gimpelev M., Mitros T., Soto C., Golgsnith-Fischman S., Kernytsky A., Schlessinger A., Koh I., Alexov E. and Honig B.\u00a0 \u201cUsing Multiple Structure Alignment, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling\u201d Proteins (2003), 53, 430-435.\r\n\r\n145)\u00a0\u00a0\u00a0 Alexov, E. \u201cRole of the Protein Side-Chain Fluctuations on the Strength of Pair-Wise Electrostatic Interactions: Comparing Experimental with Computed pKa\u2019s\u201d, Proteins (2003), 50, 94-103.\r\n\r\n146)\u00a0\u00a0\u00a0 Georgescu, R., Alexov, E. and Gunner M. \u201cCombining Conformational Flexibility and Continuum Electrostatics for Calculating pKa\u2019s in Proteins\u201d Biophys. J. (2002), 83, 1731-1748.\r\n\r\n147)\u00a0\u00a0\u00a0 J. Tandory, P. Maroti, E. Alexov, P. Sebban and L. Baciou \u201cKey role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides\u201d PNAS (2002), 99, 6702-6706.\r\n\r\n148)\u00a0\u00a0\u00a0 J. Tandory, L. Baciou, E. Alexov, P. Maroti, M. Schiffer, D. Hanson and P. Sebban \u201cRevealing the Involvement of Extended Hydrogen Bond Networks in the Cooperative Function between Distant Sites in Bacterial Reaction Center\u201d, J. Biol. Chem. (2001), 276, 45513-45515.\r\n\r\n149)\u00a0\u00a0\u00a0 Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A. and Honig, B. \u201c Rapid grid-based Construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: application to the molecular systems and geometrical objects\u201d, J. Comp. Chem. (2002), 23, 1-10.\r\n\r\n150)\u00a0\u00a0\u00a0 Alexov, E. and Honig, B. \u201cStructural and Energetic Basis of Molecular Recognition\u201d in Handbook of Cell Signaling (2002), R. Bradshaw and E. A. Dennis, Editors, Academic Press, San Diego, CA. p.11-13.\r\n\r\n151)\u00a0\u00a0\u00a0 Rocchia, W., Alexov, E. and Honig, B. \u201cExtending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions\u201d, J. Phys. Chem. (2001), 105, 6507-6514.\r\n\r\n152)\u00a0\u00a0\u00a0 Alexov, E., Valerio-Lepinies, M., Baciou, L., Schiffer, M., Hadson, D.K, Sebban, P. and Gunner, M. \"Modeling the effects of mutations within QB pocket in reaction center proteins\", Biochemistry\u00a0 (2000), 39, 5940-5952.\r\n\r\n153)\u00a0\u00a0\u00a0 Gunner, M. and Alexov, E.\" A pragmatic approach to structure based calculations of coupled proton and electron transfer in proteins\", Biochimica at Biophysica Acta (2000), 44819 , 1-25.\r\n\r\n154)\u00a0\u00a0\u00a0 Alexov, E. and Gunner, M. \"Calculating protein and proton motions coupled to electron transfer: The electron transfer from QA to QB in photosynthetic reaction centers from Rb. Sphaeroides\", Biochemistry, (1999), 38 (26) 8253-8270.\r\n\r\n155)\u00a0\u00a0\u00a0 Miteva, M. , Alexov , E. and Atanasov, B. Numerical simulation of aldolase tetramer stability, Eur. Biophys. J.\u00a0 (1998), 28, 67-73.\r\n\r\n156)\u00a0\u00a0\u00a0 Gunner, M.R. and Alexov, E. (1997) The role of the protein in modulating cofactor electrochemistry in proteins: The calculation of electrostatic forces. Molecular modeling and dynamics of bioinorganic systems. Dordrecht, Kluwer. (L. Banci and P. Comba ed.) 361-390.\r\n\r\n157)\u00a0\u00a0\u00a0 Gunner, R., Alexov, E., Torres E and Lipovaca S. The importance of the protein in controlling the electrochemistry of heme metalloproteins. Methods of calculation and analysis. J. Biol. Phys. Chem.\u00a0 (1997), 2, 126-134\r\n\r\n158)\u00a0\u00a0\u00a0 Alexov, E.G. & Gunner, M.R. \"Including protein conformational flexibility into the calculation of\u00a0 pH-dependent protein properties\", Biophys. J.\u00a0 (1997) 74, 2075-2093\r\n\r\n159)\u00a0\u00a0\u00a0 Alexov, E. ,Atanasov, B. \"Selective absorption of radio frequency energy due to collective motion of charged domains: Case of lysozyme crystal\",\u00a0 J. Biomolecular Structure and Dynamics, (1995), 13 (2), 219.\r\n\r\n160)\u00a0\u00a0\u00a0 Ohshima, H., Mishonova, E. and Alexov, E. Electrostatic interactions between two charged spheres, Biophysical Chemistry (1996), 57, 189- 203.\r\n\r\n161)\u00a0\u00a0\u00a0 Alexov, E. \"High-frequency backward waves in longitudinally magnetized gyrotropic waveguides\", Contrib. Plasma Phys. (1995), 35, 23-32.\r\n\r\n162)\u00a0\u00a0\u00a0 Alexov, E. , Atanasov, B. and Ueki, T. \"Anisotropic behavior of the pH-dependence part of Young's modulus in a lysozyme triclinic crystal\", Biopolymers (1994), 33,513 - 522.\r\n\r\n163)\u00a0\u00a0\u00a0 Alexov, E. and Mishonova, E. \"Modeling of electrostatic potential created by spherical molecule\" J. Macromolecular Science: Physics (1994), B33, 21-36.\r\n\r\n164)\u00a0\u00a0\u00a0 Alexov, E. and Atanasov, B. \"Analysis of electrostatic interactions in ribonuclease A monoclinic crystal\" Biochimica et Biophysica Acta, (1994), 1206, 55-62.\r\n\r\n165)\u00a0\u00a0\u00a0 Alexov, E.,, Ivanov, S.T. and Kapchinskii, M.I, \"Rejection band in waveguide filled with cold magnetoactive plasma\", Jpn. J. Appl. Phys. (1994),33, 5A, 2730-2734\r\n\r\n166)\u00a0\u00a0\u00a0 Ivanov S.T., Ivanova K.M. and Alexov E.G., \"Polaritons along the interface between an anysotropic semiconductor and a metallic screen\", Physica Scripta, (1994), 48, 568.\r\n\r\n167)\u00a0\u00a0\u00a0 Ivanov S.T. and Alexov E.G., \"Cherenkov generation of rayleigh electromagnetic wave in a gyrotropic plasma waveguide\", Nuclear Instruments & Methods in Physics Research (1994), A 341, 109.\r\n\r\n168)\u00a0\u00a0\u00a0 Ivanov S.T., Ivanova .M., Alexov E.G., \" Rayleigh surface waves along the boundary between a plasma and metallic screen\", J. Plasma Phys., (1993), 49, 227.\r\n\r\n169)\u00a0\u00a0\u00a0 Alexov E.G., Ivanov S.T., \"Nonreciprocal effects in a plasma waveguide\", IEEE Trans. Plasma Sci. , (1993), 21, #2 , 254 - 257.\r\n\r\n170)\u00a0\u00a0\u00a0 Alexov E.G. , \"An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma\", Phys. Scripta, (1992), 46, 429.\r\n\r\n171)\u00a0\u00a0\u00a0 Ivanov, S.T., Alexov, E. \u201cHigh-frequency electromagnetic waves in plasma waveguide\u201d, Annuaire de L\u2019Universite de Sofia (1992), 82, 113.\r\n\r\n172)\u00a0\u00a0\u00a0 Alexov E.G., Ivanov S.T., \"Anysotropic HE mode in a plasma waveguide\",\u00a0 Sov. J. Plasma Phys. (USA), 1990, 16, 493.\r\n\r\n173)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., Bogdanov A.T., Malinov P.N., \"Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field\", Plasma Phys. Control. Fusion, (1990), 32 , 791.\r\n\r\n174)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G. , Malinov E.G., \u201cSurface anisotropic plasma waves\u201d, Phys. Scripta, (1990), 42, 452.\r\n\r\n175)\u00a0\u00a0\u00a0 Ivanov S.T., Bogdanov A.T., Alexov E.G., \"A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma\", Phys. Scripta, (1990), 42, 458.\r\n\r\n176)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., \"Electromagnetic waves in a homogeneously plasma-filled\u00a0 waveguide\",\u00a0 J. Plasma Phys., (1990), 43, 51.\r\n\r\n177)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., \"Cyclotron waves in a plasma-filled waveguide\", Sov. J. Plasma Phys. (USA), 1989, 15, 657.\r\n\r\n178)\u00a0\u00a0\u00a0 Ivanov S.T, Alexov E.G., \"Electromagnetic waves in waveguide partially filled with semiconductor plasma\", Contrib. Plasma Phys., (1990), 30, 763.\r\n\r\n179)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., Malinov P.N., \"Nonsymmetrical electromagnetic waves in partially plasma - filled waveguide\", Contrib. Plasma Phys., (1990), 30, 755.\r\n\r\n180)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., \"Electromagnetic waves in the semiconductor plasma waveguide\", Phys. Scripta, (1989),40, 58.\r\n\r\n181)\u00a0\u00a0\u00a0 Ivanov S.T., Alexov E.G., Malinov P.N., \"Symmetrical electromagnetic waves in partially-filled plasma waveguide\", Plasma Phys. Control. Fusion, (1989), 31, 941.\r\n\r\n182)\u00a0\u00a0\u00a0 Alexov E.G., Ivanov S.T. \"Electromagnetic waves in plasma waveguide\", Sov. J. Plasma Phys. (USA), (1988), 14, 883.\r\n\r\n183)\u00a0\u00a0\u00a0 Aleksov, E., Ivanov, S.T., Shvachka, A.B. \u201cNumerical analysis of the electromagnetic wave dispersion in the waveguide filled with semiconductor plasma. Magnetoactive plasma\u201d, Comm. of the Joint Institute for Nuclear Research, Dubna (1984), P11-84-766.\r\n\r\n184)\u00a0\u00a0\u00a0 Aleksov, E., Ivanov, S.T., Shvachka, A.B. \u201cNumerical analysis of the electromagnetic wave dispersion in the waveguide filled with semiconductor plasma. Unmagnetized and magnetized plasma\u201d, Comm. of the Joint Institute for Nuclear Research, Dubna (1984), P11-84-592\r\n\r\n \r\n\r\nLast update 3 May 2022\r\n\r\n ","_et_gb_content_width":"","footnotes":"","_links_to":"","_links_to_target":""},"categories":[12],"tags":[],"class_list":["post-1276","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-faculty"],"_links":{"self":[{"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/posts\/1276","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/users\/32"}],"replies":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/comments?post=1276"}],"version-history":[{"count":0,"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/posts\/1276\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/media\/1275"}],"wp:attachment":[{"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/media?parent=1276"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/categories?post=1276"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/scienceweb.clemson.edu\/ihg\/wp-json\/wp\/v2\/tags?post=1276"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}