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 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.
Research
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. 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.
Publications
1) SK Panday, E Alexov, Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation, ACS omega, 2022
2) G Li, SK Panday, Y Peng, E Alexov, SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions, Bioinformatics 37 (21), 3760-3765, 2021
3) 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, 2021
4) 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–protein binding affinity, Bioinformatics 37 (7), 992-999, 10 2021
5) 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, 3, 2021
6) E Alexov, Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules, Journal of Computational Biophysics and Chemistry 20 (02), 109-110, 2021
7) 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 , 2021
8) 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
9) 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, 2021
10) 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) 3, 2021
11) 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
12) 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, 1, 2020
13) 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 2020
14) E Alexov, An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants. Genes 11 (9), 2020
15) 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
16) S Ranganathan Ganakammal, E Alexov, An ensemble approach to predict the pathogenicity of synonymous variants, Genes 11 (9), 1102, 4, 2020
17) 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
18) M Koirala, E Alexov, Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach, Journal of Theoretical and Computational Chemistry 19 (04), 2050016.
19) 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).
20) S Wang, A Lee, E Alexov, S Zhao. A regularization approach for solving Poisson’s equation with singular charge sources and diffuse interfaces. Applied Mathematics Letters 102, 106144
21) 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
22) S Pahari, G Li, AK Murthy, S Liang, R Fragoza, H Yu, E Alexov. SAAMBE-3D: Predicting Effect of Mutations on Protein–Protein Interactions. International journal of molecular sciences 21 (7), 2563
23) 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
24) 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
25) Li, Z Jia, A Chakravorty, S Pahari, Y Peng, S Basu, M Koirala, … E. Alexov. DelPhi Suite: New Developments and Review of Functionalities. Journal of Computational Chemistry 40 (28), 2502-2508
26) 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.
27) T Hazra, SA Ullah, S Wang, E Alexov, S Zhao. A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states. Journal of mathematical biology 79 (2), 631-672
28) N Tajielyato, E Alexov. Modeling pKas of unfolded proteins to probe structural models of unfolded state. Journal of Theoretical and Computational Chemistry 18 (04), 1950020
29) 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.
30) 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.
31) 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.
32) 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.
33) 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.
34) 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
35) 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.
36) 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
37) 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.
38) 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.
39) 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.
40) 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.
41) 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
42) 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.
43) 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.
44) 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
45) 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
46) 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
47) 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
48) 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
49) 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
50) 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
51) 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
52) 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
53) 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. Int J Mol Sci. 2016 Apr 7;17(4). pii: E512. doi: 10.3390/ijms17040512. PMID: 27070572
54) 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: 26988596
55) 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: 26761001
56) 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
57) 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.
58) Wang L, Zhang M, Alexov E., DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs, Bioinformatics. 2015 Oct 29. pii: btv607.
59) 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.
60) 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.
61) 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.
62) 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.
63) Emil Alexov “Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine, Advances in Biology 2015, ID 471836
64) 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
65) 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.
66) 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
67) Petukh M, Alexov E., Ion binding to biological macromolecules, Asian J Phys. 2014 Nov;23(5):735-744.
68) 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
69) 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.
70) Campbell B, Petukh M, Alexov E, Li C., On the electrostatic properties of homodimeric proteins, J Theor Comput Chem. 2014;13(3).
71) 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.
72) 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.
73) 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.
74) 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).
75) 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
76) 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
77) 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.
78) 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.
79) Alexov E, Sternberg M., Understanding molecular effects of naturally occurring genetic differences, J Mol Biol. 2013 Nov 1;425(21):3911-3.
80) Onufriev AV, Alexov E., Protonation and pK changes in protein-ligand binding. Q Rev Biophys. 2013 May;46(2):181-209.
81) 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. “A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation”, Hum Mol Genet. 2013 Sep 26.
82) Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E “Molecular Mechanisms of Disease-Causing Missense Mutations”, J Mol Biol. 2013 Jul 16. doi:pii: S0022-2836(13)00446-4. 10.1016/j.jmb.2013.07.014. [Epub ahead of print]
83) Dolzhanskaya N, Gonzalez M, Stefl S, Messing J, Wen GY, Alexov E, Zuchner S, Velinov M “A 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”, Journal of Alzheimer’s Disease, 2014;39(1):23-7. doi: 10.3233
84) Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR. “Cancer missense mutations alter binding properties of proteins and their interaction networks”, PLoS One. 2013 Jun 14;8(6):e66273.
85) Li C, Petukh M, Li L, Alexov E. “Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi”, J Comput Chem. 2013 Jun 4. doi: 10.1002/jcc.23340.
86) Zhang Z, Norris J, Kalscheuer V, Wood T, Wang L, Schwartz C, Alexov E, Van Esch H. “A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome”, Hum Mol Genet. 2013 May 31.
87) 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.
88) 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.
89) 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
90) 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]
91) Petukh M, Kimmet T, Alexov E. “BION web server: predicting non-specifically bound surface ions.” Bioinformatics. 2013 Mar 15;29(6):805-6
92) 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.
93) 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]
94) 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.
95) 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)
96) 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
97) 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
98) Lin Wang, Zhe Zhang, Walter Rocchia and Emil Alexov “Using DelPhi capabilities to mimic protein’s conformational reorganization with amino acid specific dielectric constants”, Comm. Comp. Phys., (2013), 13, 13-30
99) Sergio Decherchi, Jos´e 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
100) 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
101) 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
102) 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.
103) 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.
104) 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.
105) Mitra, R., Zhang. Zhe and Alexov, E, “In silico modeling of pH-optimum of protein-protein binding”, Proteins (2011), 171, 285-289.
106) 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.
107) 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.
108) 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.
109) 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.
110) Teng S, Srivastava AK, Schwartz CE, Alexov E, Wang L , “Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interactions”, Int J Comput Biol Drug Des. 2011;3(4):334-49.
111) Mitra, R., Zhang. Zhe and Alexov, E, “In silico modeling of pH-optimum of protein–protein binding”, Proteins (2011), 171, 285-289.
112) Talley, K. and Alexov, E. “On the pH-optimum of activity and stability”, Proteins (2010), 78, 2699-706.
113) Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E. “Computational analysis of missense mutations causing Snyder-Robinson syndrome”, Hum Mutat. (2010) 31(9):1043-9.
114) Mitra, R. and Alexov, E. “Analyzing and Predicting Protein Binding Pockets In Silico Lead Discovery, 2011, 84-98.
115) Teng, S., Madej, T., Panchenko, A. and Alexov, E. “Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions”, Biophysical Journal, (2009), 96, 2178-2188.
116) Talley Kemper, Ng Carmen, Snoppell Michael, Kundrotas Petras and Alexov E. “On the electrostatic component of protein-protein binding free energy” PMC Biophysics 2008,1:2 1-23.
117) Kosloff M., Alexov E., Arshavsky Y. and Hong B. “Electrostatic and Lipid Anchor Contributions to the Interaction of Transduin with Membrane” The Journal of Biological Chemistry 283(2008) 31197-31207.
118) Mitra, R, Shyam, R., Mitra, I., Miteva, M. and Alexov, E “Calculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions” Current Computer-Aided Drug Design: 4: 169-179.
119) Kundrotas, P, Lensink, M. and Alexov, E. “Homology-based modeling of 3D structures of protein-protein complexes using alignment of modified sequence profiles”, Int. J. Biol. Macromol. (2008), 43: 198-208.
120) Alexov, E. “ Editorial”, Current Pharmaceutical Biotechnology (2008) 9:55-56.
121) Miteva, A.Maria, Alexov , Emil, Villoutreix, Bruno.O “Protein Structure Analysis Online” Current Protocols in Protein Science (2007) 2:13:1-23.
122) Teng S., Michonova-Alexova E and Alexov, E. “Approaches and Resources for prediction of the Effects of Non-Synonymous Single Nucleotide Polymorphism on Protein Function and Intearctions” Current Pharmaceutical Biotechnology (2008) 9:123-133.
123) Talley, K., Kundrotas, P. and Alexov, E. “Modeling Salt Dependence of Protein-Protein Association: Linear vs Non-Linear Poisson-Boltzmann Equation”. Comm. Comp. Phys. (2008), 3: 1071.
124) Kundrotas P. and Alexov E. “Predicting interacting and interfacial residues using continuous sequence segments” Int J Biol Macromol. 2007 Dec 1;41(5):615-23. Epub 2007 Aug 9.
125) Brook K., Talley. K., Coley. K., Kundrotas P., Alexov. E. “Optimization of electrostatic interactions in protein-protein complexes”. Biophys J. 2007 Nov 15;93(10):3340-52. Epub 2007 Aug 10.
126) Augustin Ofiretu, Nadia Bucurenci, Emil Alexov, Thomas Bertrand, Pierre Briozzo, Helene Munier-Lehmann and Anne-Marie Gilles “Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase”, FEBS Letters (2007) 274, 3363–3373.
127) Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. “Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families ” J. Bioinformatics and Comp. Biol. (2007), 5, 693-715.
128) Kundrotas, P., Georgieva, P., Shosheva, A., Christova, P. and Alexov, E. “BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families”, Int. J. Biol. Macromol.(2007), Jun 1;41(1):114-9.
129) C. L. Tang, E. Alexov, A. Pyle and B. Honig “Calculation of pKas in RNA: On the structural origins and functional roles of protonated nucleotides”, J. Mol. Biol. (2007), Mar 9; 366(5):1475-96.
130) Claudia, B., Honig, B. and Alexov, E. “Poisson-Boltzmann calculations of non-specific salt effects on protein-protein binding free energies”, Biophys. J. (2007), Mar 15; 92(6):1891-9.
131) Isvoran, A., Craescu, C. and Alexov, E. “Electrostatic control of the overall shape of calmodulin: numerical calculations” Eur. Biophys. J (2007) Mar; 36(3):225-37.
132) Kundrotas, P.J. and Alexov, E. “Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives” BMC Bioinformatics, 2006. 7(1): p. 503.
133) Kundrotas, P. and Alexov, E “ProtCom: Searchable database of protein-protein complexes” Nuclear Acids Research (2007) 35. D575-D579.
134) Kundrotas, P. and Alexov, E “Predicting 3D structures of transient protein-protein complexes by homology” Biochimica at Biophysica Acta (2006), 1764, 1498-1511.
135) Kundrotas, P. and Alexov, E “Electrostatic properties of protein-protein complexes” Biophys. J. (2006), 91, 1724-1736.
136) Wu Y, Hudson JS, Lu Q, Moore JM, Mount AS, Rao AM, Alexov E, Ke PC. “Coating single-walled carbon nanotubes with phospholipids”, J Phys Chem B (2006), 110(6):2475-2478.
137) Grey MJ, Tang Y, Alexov E, McKnight CJ, Raleigh DP, Palmer AG 3rd. “Characterizing 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” J Mol Biol (2006) 355:1078-1094.
138) Shosheva, A., Donchev, A., Dimitrov, M., Kostov, G., Toromanov, G., Getov, V and E. Alexov “Comparative study of the stability of poplar plastocyanin isoforms” Biochimica et Biophysica Acta (2005), 1748, 116-127
139) Zhu, J., Alexov, E. and B. Honig “Comparative Study of Generalized Born Models: Born Radii and Peptide Folding” J. Phys. Chem. B (2005) 109, 3008-3022.
140) Alexov, E. “Calculating 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” Proteins (2004), 56, 572-584.
141) Tang C., Xie L., Koh I., Posy S., Alexov E. and Honig B. “On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles” J. Mol. Biol. (2003), 334, 1043-1062.
142) Shosheva, A., Donchev, A., Dimitrov, M., Zlatanav, I., Toromanov, G., Getov, V. and Alexov, E. “Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity” Biochemica at Biophysica Acta (2004), 1698, 67-75.
143) Alexov, E. “Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure” Eur. J. Biochem. (2004), 271, 173-185.
144) 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. “Using Multiple Structure Alignment, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling” Proteins (2003), 53, 430-435.
145) Alexov, E. “Role of the Protein Side-Chain Fluctuations on the Strength of Pair-Wise Electrostatic Interactions: Comparing Experimental with Computed pKa’s”, Proteins (2003), 50, 94-103.
146) Georgescu, R., Alexov, E. and Gunner M. “Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKa’s in Proteins” Biophys. J. (2002), 83, 1731-1748.
147) J. Tandory, P. Maroti, E. Alexov, P. Sebban and L. Baciou “Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides” PNAS (2002), 99, 6702-6706.
148) J. Tandory, L. Baciou, E. Alexov, P. Maroti, M. Schiffer, D. Hanson and P. Sebban “Revealing the Involvement of Extended Hydrogen Bond Networks in the Cooperative Function between Distant Sites in Bacterial Reaction Center”, J. Biol. Chem. (2001), 276, 45513-45515.
149) Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A. and Honig, B. “ 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”, J. Comp. Chem. (2002), 23, 1-10.
150) Alexov, E. and Honig, B. “Structural and Energetic Basis of Molecular Recognition” in Handbook of Cell Signaling (2002), R. Bradshaw and E. A. Dennis, Editors, Academic Press, San Diego, CA. p.11-13.
151) Rocchia, W., Alexov, E. and Honig, B. “Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions”, J. Phys. Chem. (2001), 105, 6507-6514.
152) 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 (2000), 39, 5940-5952.
153) 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.
154) 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.
155) Miteva, M. , Alexov , E. and Atanasov, B. Numerical simulation of aldolase tetramer stability, Eur. Biophys. J. (1998), 28, 67-73.
156) 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.
157) 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. (1997), 2, 126-134
158) Alexov, E.G. & Gunner, M.R. “Including protein conformational flexibility into the calculation of pH-dependent protein properties”, Biophys. J. (1997) 74, 2075-2093
159) Alexov, E. ,Atanasov, B. “Selective absorption of radio frequency energy due to collective motion of charged domains: Case of lysozyme crystal”, J. Biomolecular Structure and Dynamics, (1995), 13 (2), 219.
160) Ohshima, H., Mishonova, E. and Alexov, E. Electrostatic interactions between two charged spheres, Biophysical Chemistry (1996), 57, 189- 203.
161) Alexov, E. “High-frequency backward waves in longitudinally magnetized gyrotropic waveguides”, Contrib. Plasma Phys. (1995), 35, 23-32.
162) 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.
163) Alexov, E. and Mishonova, E. “Modeling of electrostatic potential created by spherical molecule” J. Macromolecular Science: Physics (1994), B33, 21-36.
164) Alexov, E. and Atanasov, B. “Analysis of electrostatic interactions in ribonuclease A monoclinic crystal” Biochimica et Biophysica Acta, (1994), 1206, 55-62.
165) 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
166) 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.
167) 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.
168) 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.
169) Alexov E.G., Ivanov S.T., “Nonreciprocal effects in a plasma waveguide”, IEEE Trans. Plasma Sci. , (1993), 21, #2 , 254 – 257.
170) 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.
171) Ivanov, S.T., Alexov, E. “High-frequency electromagnetic waves in plasma waveguide”, Annuaire de L’Universite de Sofia (1992), 82, 113.
172) Alexov E.G., Ivanov S.T., “Anysotropic HE mode in a plasma waveguide”, Sov. J. Plasma Phys. (USA), 1990, 16, 493.
173) 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.
174) Ivanov S.T., Alexov E.G. , Malinov E.G., “Surface anisotropic plasma waves”, Phys. Scripta, (1990), 42, 452.
175) 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.
176) Ivanov S.T., Alexov E.G., “Electromagnetic waves in a homogeneously plasma-filled waveguide”, J. Plasma Phys., (1990), 43, 51.
177) Ivanov S.T., Alexov E.G., “Cyclotron waves in a plasma-filled waveguide”, Sov. J. Plasma Phys. (USA), 1989, 15, 657.
178) Ivanov S.T, Alexov E.G., “Electromagnetic waves in waveguide partially filled with semiconductor plasma”, Contrib. Plasma Phys., (1990), 30, 763.
179) Ivanov S.T., Alexov E.G., Malinov P.N., “Nonsymmetrical electromagnetic waves in partially plasma – filled waveguide”, Contrib. Plasma Phys., (1990), 30, 755.
180) Ivanov S.T., Alexov E.G., “Electromagnetic waves in the semiconductor plasma waveguide”, Phys. Scripta, (1989),40, 58.
181) Ivanov S.T., Alexov E.G., Malinov P.N., “Symmetrical electromagnetic waves in partially-filled plasma waveguide”, Plasma Phys. Control. Fusion, (1989), 31, 941.
182) Alexov E.G., Ivanov S.T. “Electromagnetic waves in plasma waveguide”, Sov. J. Plasma Phys. (USA), (1988), 14, 883.
183) Aleksov, E., Ivanov, S.T., Shvachka, A.B. “Numerical analysis of the electromagnetic wave dispersion in the waveguide filled with semiconductor plasma. Magnetoactive plasma”, Comm. of the Joint Institute for Nuclear Research, Dubna (1984), P11-84-766.
184) Aleksov, E., Ivanov, S.T., Shvachka, A.B. “Numerical analysis of the electromagnetic wave dispersion in the waveguide filled with semiconductor plasma. Unmagnetized and magnetized plasma”, Comm. of the Joint Institute for Nuclear Research, Dubna (1984), P11-84-592
Last update 3 May 2022