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Last Name
Institution

Emil Georgiev Alexov

TitleProfessor
InstitutionClemson University
DepartmentDepartment of Physics & Astronomy
Address118 Kinard Laboratory
Clemson, South Carolina 29634
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Li C, Jia Z, Chakravorty A, Pahari S, Peng Y, Basu S, Koirala M, Panday SK, Petukh M, Li L, Alexov E. DelPhi Suite: New Developments and Review of Functionalities. J Comput Chem. 2019 Jun 25. PMID: 31237360.
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    2. Hazra T, Ahmed Ullah S, Wang S, Alexov E, Zhao S. A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states. J Math Biol. 2019 Jul; 79(2):631-672. PMID: 31030299.
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    3. 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 Jun; 64(6):561-572. PMID: 30858506.
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    4. Tajielyato N, Alexov E. Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. Int J Mol Sci. 2019 Mar 03; 20(5). PMID: 30832428.
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    5. 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 05; 40(12):1290-1304. PMID: 30698861.
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    6. 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). PMID: 30696058.
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    7. Pahari S, Sun L, Alexov E. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database (Oxford). 2019 01 01; 2019. PMID: 30805645.
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    8. Pahari S, Sun L, Basu S, Alexov E. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins. 2018 12; 86(12):1277-1283. PMID: 30252159.
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    9. 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 05; 8(1):13266. PMID: 30185874.
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    10. 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; 5:25. PMID: 29637074.
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    11. 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 03 01; 34(5):779-786. PMID: 29091991.
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    12. 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. PMID: 29350933.
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    13. 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 03; 26(3):420-427. PMID: 29358613.
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    14. 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 04; 19(1). PMID: 29300326.
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    15. 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. PMID: 29036596.
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    16. 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 08 15; 7(1):8237. PMID: 28811629.
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    17. Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem. 2017 08 15; 38(22):1974-1979. PMID: 28602026.
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    18. 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 04 18; 56(15):2149-2160. PMID: 28318265.
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    19. 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-linked ß-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability. J Biol Chem. 2017 05 26; 292(21):8948-8963. PMID: 28302723.
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    20. 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 03 07; 33(9):2283-2295. PMID: 28181811.
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    21. Li L, Chakravorty A, Alexov E. DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem. 2017 04 05; 38(9):584-593. PMID: 28130775.
      View in: PubMed
    22. 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. PMID: 27936518.
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    23. Peng Y, Alexov E. Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. Proteins. 2016 12; 84(12):1797-1809. PMID: 27696497.
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    24. Chakavorty A, Li L, Alexov E. Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. J Comput Chem. 2016 10 30; 37(28):2495-507. PMID: 27546093.
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    25. Li L, Alper J, Alexov E. Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions. Sci Rep. 2016 08 17; 6:31523. PMID: 27531742.
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    26. 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 10 21; 11(10):2706-2715. PMID: 27356039.
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    27. 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):547. PMID: 27077847.
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    28. 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 07; 17(4):512. PMID: 27070572.
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    29. 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. PMID: 26988596.
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    30. Peng Y, Alexov E. Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. Proteins. 2016 Feb; 84(2):232-9. PMID: 26650512.
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    31. 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 08; 17(1). PMID: 26761001.
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    32. 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. PMID: 26580603.
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    33. Wang L, Zhang M, Alexov E. DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs. Bioinformatics. 2016 Feb 15; 32(4):614-5. PMID: 26515825.
      View in: PubMed
    34. 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 Dec 15; 36(32):2381-93. PMID: 26484964.
      View in: PubMed
    35. Wang L, Li L, Alexov E. pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa. Proteins. 2015 Dec; 83(12):2186-97. PMID: 26408449.
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    36. 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. PMID: 26418480.
      View in: PubMed
    37. 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; 11(7):e1004276. PMID: 26146996.
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    38. 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 01; 24(17):4848-61. PMID: 26056227.
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    39. 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):524-534. PMID: 25689729.
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    40. Kucukkal TG, Alexov E. Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. Comput Math Methods Med. 2015; 2015:746157. PMID: 26064184.
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    41. Li L, Wang L, Alexov E. On the energy components governing molecular recognition in the framework of continuum approaches. Front Mol Biosci. 2015; 2:5. PMID: 25988173.
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    42. 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. PMID: 25658850.
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    43. 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; 9(11):e111604. PMID: 25369028.
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    44. Petukh M, Alexov E. Ion binding to biological macromolecules. Asian J Phys. 2014 Nov; 23(5):735-744. PMID: 25774076.
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    45. 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; 9(10):e110884. PMID: 25340632.
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    46. 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. PMID: 25126110.
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    47. 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. PMID: 24886813.
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    48. Dias RP, Lin 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):1418-1429. PMID: 24799021.
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    49. 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. PMID: 24794930.
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    50. 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). PMID: 25018579.
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    51. 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 08; 10(4):1770-1780. PMID: 24803870.
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    52. Campbell B, Petukh M, Alexov E, Li C. On the electrostatic properties of homodimeric proteins. J Theor Comput Chem. 2014; 13(3). PMID: 25419028.
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    53. Dolzhanskaya N, Gonzalez MA, Sperziani F, Stefl S, Messing J, Wen GY, Alexov E, Zuchner S, Velinov M. A novel p.Leu(381)Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease. J Alzheimers Dis. 2014; 39(1):23-7. PMID: 24121961.
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    54. 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. 2014 Jan 15; 23(2):418-33. PMID: 24026681.
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    55. Alexov E, Sternberg M. Understanding molecular effects of naturally occurring genetic differences. J Mol Biol. 2013 Nov 01; 425(21):3911-3. PMID: 23968859.
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    56. Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. J Mol Biol. 2013 Nov 01; 425(21):3919-36. PMID: 23871686.
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    57. 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; 8(6):e66273. PMID: 23799087.
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    58. 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 Aug 15; 34(22):1949-60. PMID: 23733490.
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    59. 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 Sep 15; 22(18):3789-97. PMID: 23696453.
      View in: PubMed
    60. Onufriev AV, Alexov E. Protonation and pK changes in protein-ligand binding. Q Rev Biophys. 2013 May; 46(2):181-209. PMID: 23889892.
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    61. 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 09; 9(4):2126-2136. PMID: 23585741.
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    62. Li C, Li L, Petukh M, Alexov E. Progress in developing Poisson-Boltzmann equation solvers. Mol Based Math Biol. 2013 Mar 01; 1. PMID: 24199185.
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    63. Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E. Enhancing human spermine synthase activity by engineered mutations. PLoS Comput Biol. 2013; 9(2):e1002924. PMID: 23468611.
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    64. 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 Jul-Aug; 20(4):643-51. PMID: 23408511.
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    65. Petukh M, Kimmet T, Alexov E. BION web server: predicting non-specifically bound surface ions. Bioinformatics. 2013 Mar 15; 29(6):805-6. PMID: 23380591.
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    66. Petukh M, Stefl S, Alexov E. The role of protonation states in ligand-receptor recognition and binding. Curr Pharm Des. 2013; 19(23):4182-90. PMID: 23170880.
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    67. Wang L, Zhang Z, Rocchia W, Alexov E. Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants. Commun Comput Phys. 2013 Jan; 13(1):13-30. PMID: 24683422.
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    68. Wang L, Witham S, Zhang Z, Li L, Hodsdon ME, Alexov E. In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor. Commun Comput Phys. 2013 Jan; 13(1):207-222. PMID: 24683423.
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    69. Sarkar S, Witham S, Zhang J, Zhenirovskyy M, Rocchia W, Alexov E. DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Commun Comput Phys. 2013 Jan; 13(1):269-284. PMID: 24683424.
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    70. Decherchi S, Colmenares J, Catalano CE, Spagnuolo M, Alexov E, Rocchia W. Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution. Commun Comput Phys. 2013 Jan 01; 13:61-89. PMID: 23519863.
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    71. 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 05; 12:31. PMID: 23217202.
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    72. Takano K, Liu 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 Oct 15; 21(20):4497-507. PMID: 22814392.
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    73. 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):2885-93. PMID: 22735539.
      View in: PubMed
    74. 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. PMID: 22674480.
      View in: PubMed
    75. 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 May 14; 5:9. PMID: 22583952.
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    76. Smith N, Witham S, Sarkar S, Zhang J, Li L, Li C, Alexov E. DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. Bioinformatics. 2012 Jun 15; 28(12):1655-7. PMID: 22531215.
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    77. Zhang Z, Miteva MA, Wang L, Alexov E. Analyzing effects of naturally occurring missense mutations. Comput Math Methods Med. 2012; 2012:805827. PMID: 22577471.
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    78. Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E. Predicting folding free energy changes upon single point mutations. Bioinformatics. 2012 Mar 01; 28(5):664-71. PMID: 22238268.
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    79. Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MH, Shen JK, Warwicker J, Williams S, Word JM. Progress in the prediction of pKa values in proteins. Proteins. 2011 Dec; 79(12):3260-75. PMID: 22002859.
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    80. Witham S, Talley K, Wang L, Zhang Z, Sarkar S, Gao D, Yang W, Alexov E. Developing hybrid approaches to predict pKa values of ionizable groups. Proteins. 2011 Dec; 79(12):3389-99. PMID: 21744395.
      View in: PubMed
    81. Witham S, Takano K, Schwartz C, 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 Aug; 79(8):2444-54. PMID: 21630357.
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    82. Zhang Z, Norris J, Schwartz C, 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. PMID: 21647366.
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    83. Zhang Z, Witham S, Alexov E. On the role of electrostatics in protein-protein interactions. Phys Biol. 2011 Jun; 8(3):035001. PMID: 21572182.
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    84. 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 interaction. Int J Comput Biol Drug Des. 2010; 3(4):334-49. PMID: 21297231.
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    85. Mitra RC, Zhang Z, Alexov E. In silico modeling of pH-optimum of protein-protein binding. Proteins. 2011 Mar; 79(3):925-36. PMID: 21287623.
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    86. Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E. Computational analysis of missense mutations causing Snyder-Robinson syndrome. Hum Mutat. 2010 Sep; 31(9):1043-9. PMID: 20556796.
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    87. Talley K, Alexov E. On the pH-optimum of activity and stability of proteins. Proteins. 2010 Sep; 78(12):2699-706. PMID: 20589630.
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    88. Teng S, Madej T, Panchenko A, Alexov E. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J. 2009 Mar 18; 96(6):2178-88. PMID: 19289044.
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    89. Talley K, Ng C, Shoppell M, Kundrotas P, Alexov E. On the electrostatic component of protein-protein binding free energy. PMC Biophys. 2008 Nov 05; 1(1):2. PMID: 19351424.
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    90. Kosloff M, Alexov E, Arshavsky VY, Honig B. Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. J Biol Chem. 2008 Nov 07; 283(45):31197-207. PMID: 18782760.
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    91. Kundrotas PJ, Lensink MF, Alexov E. Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles. Int J Biol Macromol. 2008 Aug 15; 43(2):198-208. PMID: 18572239.
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    92. Alexov E. Protein-protein interactions. Curr Pharm Biotechnol. 2008 Apr; 9(2):55-6. PMID: 18393861.
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    93. Teng S, Michonova-Alexova E, Alexov E. Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Curr Pharm Biotechnol. 2008 Apr; 9(2):123-33. PMID: 18393868.
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    94. Miteva MA, Alexov E, Villoutreix BO. Protein structure analysis online. Curr Protoc Protein Sci. 2007 Nov; Chapter 2:Unit 2.13. PMID: 18429316.
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    95. Brock 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. PMID: 17693468.
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    96. Kundrotas P, Alexov E. Predicting interacting and interfacial residues using continuous sequence segments. Int J Biol Macromol. 2007 Dec 01; 41(5):615-23. PMID: 17850859.
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    97. Ofiteru A, Bucurenci N, Alexov E, Bertrand T, Briozzo P, Munier-Lehmann H, Gilles AM. Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase. FEBS J. 2007 Jul; 274(13):3363-73. PMID: 17542990.
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    98. Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E. Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families. J Bioinform Comput Biol. 2007 Jun; 5(3):693-715. PMID: 17688312.
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    99. Isvoran A, Craescu CT, Alexov E. Electrostatic control of the overall shape of calmodulin: numerical calculations. Eur Biophys J. 2007 Mar; 36(3):225-37. PMID: 17285296.
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    100. Kundrotas P, Georgieva P, Shosheva A, Christova P, 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 01; 41(1):114-9. PMID: 17320167.
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    101. Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J. 2007 Mar 15; 92(6):1891-9. PMID: 17208980.
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    102. Tang CL, Alexov E, Pyle AM, Honig B. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. J Mol Biol. 2007 Mar 09; 366(5):1475-96. PMID: 17223134.
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    103. Kundrotas PJ, Alexov EG. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinformatics. 2006 Nov 16; 7:503. PMID: 17109752.
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    104. Kundrotas PJ, Alexov E. PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. 2007 Jan; 35(Database issue):D575-9. PMID: 17071962.
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    105. Kundrotas PJ, Alexov E. Predicting 3D structures of transient protein-protein complexes by homology. Biochim Biophys Acta. 2006 Sep; 1764(9):1498-511. PMID: 16963323.
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    106. Kundrotas PJ, Alexov E. Electrostatic properties of protein-protein complexes. Biophys J. 2006 Sep 01; 91(5):1724-36. PMID: 16782791.
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    107. 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 Feb 16; 110(6):2475-8. PMID: 16471843.
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    108. Grey MJ, Tang Y, Alexov E, McKnight CJ, Raleigh DP, Palmer AG. 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 Feb 03; 355(5):1078-94. PMID: 16332376.
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    109. Zhu J, Alexov E, Honig B. Comparative study of generalized born models: Born radii and peptide folding. J Phys Chem B. 2005 Feb 24; 109(7):3008-22. PMID: 16851315.
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    110. Shosheva A, Donchev A, Dimitrov M, Kostov G, Toromanov G, Getov V, Alexov E. Comparative study of the stability of poplar plastocyanin isoforms. Biochim Biophys Acta. 2005 Apr 15; 1748(1):116-27. PMID: 15752700.
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    111. 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 Aug 15; 56(3):572-84. PMID: 15229889.
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    112. Shosheva A, Donchev A, Dimitrov M, Zlatanov I, Toromanov G, Getov V, Alexov E. Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity. Biochim Biophys Acta. 2004 Apr 08; 1698(1):67-75. PMID: 15063316.
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    113. 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 Jan; 271(1):173-85. PMID: 14686930.
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    114. Tang CL, Xie L, Koh IY, Posy S, Alexov E, 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 Dec 12; 334(5):1043-62. PMID: 14643665.
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    115. Alexov E. Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s. Proteins. 2003 Jan 01; 50(1):94-103. PMID: 12471602.
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    116. Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 2003; 53 Suppl 6:430-5. PMID: 14579332.
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    117. Georgescu RE, Alexov EG, Gunner MR. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys J. 2002 Oct; 83(4):1731-48. PMID: 12324397.
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    118. Tandori J, Maroti P, Alexov E, Sebban P, Baciou L. Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides. Proc Natl Acad Sci U S A. 2002 May 14; 99(10):6702-6. PMID: 11983861.
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    119. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem. 2002 Jan 15; 23(1):128-37. PMID: 11913378.
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    120. Tandori J, Baciou L, Alexov E, Maroti P, Schiffer M, Hanson DK, Sebban P. Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers. J Biol Chem. 2001 Dec 07; 276(49):45513-5. PMID: 11604387.
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    121. Alexov E, Miksovska J, Baciou L, Schiffer M, Hanson DK, Sebban P, Gunner MR. Modeling the effects of mutations on the free energy of the first electron transfer from QA- to QB in photosynthetic reaction centers. Biochemistry. 2000 May 23; 39(20):5940-52. PMID: 10821665.
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    122. Gunner MR, Alexov E. A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Biochim Biophys Acta. 2000 May 12; 1458(1):63-87. PMID: 10812025.
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    123. Alexov EG, Gunner MR. Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers. Biochemistry. 1999 Jun 29; 38(26):8253-70. PMID: 10387071.
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    124. Alexov EG, Gunner MR. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys J. 1997 May; 72(5):2075-93. PMID: 9129810.
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    125. Ohshima H, Mishonova E, Alexov E. Electrostatic interaction between two charged spherical molecules. Biophys Chem. 1996 Jan; 57(2-3):189-203. PMID: 17023339.
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    126. Alexov E, Atanasov B. Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal. J Biomol Struct Dyn. 1995 Oct; 13(2):219-28. PMID: 8579783.
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    127. Alexov E, Atanasov B. Analysis of electrostatic interactions in ribonuclease A monoclinic crystal. Biochim Biophys Acta. 1994 May 18; 1206(1):55-62. PMID: 8186250.
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