| Year |
Citation |
Score |
| 2024 |
Rimal P, Panday SK, Xu W, Peng Y, Alexov E. SAAMBE-MEM: A Sequence-Based Method for Predicting Binding Free Energy Change upon Mutation in Membrane Protein-Protein Complexes. Bioinformatics (Oxford, England). PMID 39240325 DOI: 10.1093/bioinformatics/btae544 |
0.333 |
|
| 2024 |
Pandey P, Alexov E. Most Monogenic Disorders Are Caused by Mutations Altering Protein Folding Free Energy. International Journal of Molecular Sciences. 25. PMID 38396641 DOI: 10.3390/ijms25041963 |
0.32 |
|
| 2023 |
Pandey P, Alexov E. Most monogenic disorders are caused by mutations altering protein folding free energy. Research Square. PMID 37886551 DOI: 10.21203/rs.3.rs-3442589/v1 |
0.319 |
|
| 2023 |
Pandey P, Panday SK, Rimal P, Ancona N, Alexov E. Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations. International Journal of Molecular Sciences. 24. PMID 37569449 DOI: 10.3390/ijms241512073 |
0.352 |
|
| 2020 |
Ganakammal SR, Alexov E. An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants Genes. 11: 1102. PMID 32967157 DOI: 10.3390/Genes11091102 |
0.308 |
|
| 2020 |
Li G, Pahari S, Krishna Murthy A, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-SEQ: A Sequence-based Method for Predicting Mutation Effect on Protein-protein Binding Affinity. Bioinformatics (Oxford, England). PMID 32866236 DOI: 10.1093/Bioinformatics/Btaa761 |
0.436 |
|
| 2020 |
Lee YR, Khan K, Armfield-Uhas K, Srikanth S, Thompson NA, Pardo M, Yu L, Norris JW, Peng Y, Gripp KW, Aleck KA, Li C, Spence E, Choi TI, Kwon SJ, ... ... Alexov E, et al. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy. Nature Communications. 11: 3698. PMID 32703943 DOI: 10.1038/S41467-020-17452-6 |
0.308 |
|
| 2020 |
Pahari S, Li G, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. International Journal of Molecular Sciences. 21. PMID 32272725 DOI: 10.3390/Ijms21072563 |
0.394 |
|
| 2020 |
Chakravorty A, Pandey S, Pahari S, Zhao S, Alexov E. 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. PMID 32155062 DOI: 10.1021/Acs.Jcim.0C00151 |
0.341 |
|
| 2020 |
Koirala M, Alexov E. Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach Journal of Theoretical and Computational Chemistry. 19: 2050016. DOI: 10.1142/S0219633620500169 |
0.33 |
|
| 2020 |
Ganakammal SR, Koirala M, Wu B, Alexov E. In-silico analysis to identify the role of MEN1 missense mutations in breast cancer Journal of Theoretical and Computational Chemistry. 19: 2041002. DOI: 10.1142/S0219633620410023 |
0.311 |
|
| 2020 |
Koirala M, Alexov E. Computational Analysis of Missense Mutations in Creatine Transporter Protein Associated with Creatine Deficiency Syndrome Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.1190 |
0.337 |
|
| 2019 |
Shashikala HBM, Chakravorty A, Alexov E. Modeling Electrostatic Force in Protein-Protein Recognition. Frontiers in Molecular Biosciences. 6: 94. PMID 31608289 DOI: 10.3389/Fmolb.2019.00094 |
0.369 |
|
| 2019 |
Peng Y, Yang Y, Li L, Jia Z, Cao W, Alexov E. DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme. Frontiers in Molecular Biosciences. 6: 74. PMID 31552265 DOI: 10.3389/Fmolb.2019.00074 |
0.323 |
|
| 2019 |
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. Journal of Mathematical Biology. PMID 31030299 DOI: 10.1007/S00285-019-01372-1 |
0.365 |
|
| 2019 |
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? Journal of Human Genetics. PMID 30858506 DOI: 10.1038/S10038-019-0585-5 |
0.395 |
|
| 2019 |
Tajielyato N, Alexov E. Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. International Journal of Molecular Sciences. 20: 1090. PMID 30832428 DOI: 10.3390/Ijms20051090 |
0.328 |
|
| 2019 |
Pahari S, Sun L, Alexov E. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database : the Journal of Biological Databases and Curation. 2019. PMID 30805645 DOI: 10.1093/Database/Baz024 |
0.382 |
|
| 2019 |
Chakravorty A, Gallicchio E, Alexov E. A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. Journal of Computational Chemistry. PMID 30698861 DOI: 10.1002/Jcc.25786 |
0.323 |
|
| 2019 |
Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. International Journal of Molecular Sciences. 20. PMID 30696058 DOI: 10.3390/Ijms20030548 |
0.445 |
|
| 2019 |
Panday SK, Shashikala MHB, Chakravorty A, Zhao S, Alexov E. Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes Communications in Information and Systems. 19: 405-423. DOI: 10.4310/Cis.2019.V19.N4.A4 |
0.383 |
|
| 2019 |
Tajielyato N, Alexov E. Modeling pKas of unfolded proteins to probe structural models of unfolded state Journal of Theoretical and Computational Chemistry. 18: 1950020. DOI: 10.1142/S0219633619500202 |
0.34 |
|
| 2019 |
Pahari S, Sun L, Alexov E. Surface-Free Protocol for Computing PKA's (DelPhiPKa): Applications to Protein-Protein Interactions Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.924 |
0.341 |
|
| 2019 |
Chakravorty A, Higham J, Alexov E, Henchman RH. New Method to Determine the Effect of Dimerization on Protein Flexibility from Molecular Dynamics Simulation using Structural Hierarchy Biophysical Journal. 116: 561a-562a. DOI: 10.1016/J.Bpj.2018.11.3019 |
0.326 |
|
| 2019 |
Bosthanthirige MSH, Chakravorty A, Alexov E. Modeling Electrostatic Force in Protein-Protein Recognition Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.291 |
0.337 |
|
| 2018 |
Pahari S, Sun L, Basu S, Alexov E. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins. PMID 30252159 DOI: 10.1002/Prot.25608 |
0.35 |
|
| 2018 |
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. Scientific Reports. 8: 13266. PMID 30185874 DOI: 10.1038/S41598-018-31480-9 |
0.338 |
|
| 2018 |
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. Frontiers in Molecular Biosciences. 5: 25. PMID 29637074 DOI: 10.3389/Fmolb.2018.00025 |
0.331 |
|
| 2018 |
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. Journal of Chemical Theory and Computation. PMID 29350933 DOI: 10.1021/Acs.Jctc.7B00756 |
0.345 |
|
| 2018 |
Peng Y, Myers R, Zhang W, Alexov E. Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome. International Journal of Molecular Sciences. 19. PMID 29300326 DOI: 10.3390/Ijms19010141 |
0.39 |
|
| 2018 |
Jia Z, Li L, Peng Y, Ding F, Alexov E. The capricious electrostatic force: Revealing the signaling pathway in integrin α2-I domain Journal of Theoretical and Computational Chemistry. 17: 1840001. DOI: 10.1142/S0219633618400011 |
0.324 |
|
| 2018 |
Godar SC, Lovelace H, Eller J, Spencer M, Li L, Hamilton G, Sanabria H, Alexov E, Alper J. Single Molecule Study of Long-Range Electrostatic Binding Affinity of Cytoplasmic Dynein's Microtubule Binding Domain Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.2800 |
0.304 |
|
| 2017 |
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 (Oxford, England). PMID 29091991 DOI: 10.1093/Bioinformatics/Btx698 |
0.398 |
|
| 2017 |
Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E. DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinformatics (Oxford, England). PMID 29036596 DOI: 10.1093/Bioinformatics/Btx495 |
0.336 |
|
| 2017 |
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. Scientific Reports. 7: 8237. PMID 28811629 DOI: 10.1038/S41598-017-08419-7 |
0.351 |
|
| 2017 |
Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. Journal of Computational Chemistry. PMID 28602026 DOI: 10.1002/Jcc.24831 |
0.328 |
|
| 2017 |
Hoffman L, Li L, Alexov E, Sanabria H, Waxham MN. Cytoskeletal-like filaments of CaMKII are formed in a regulated and Zn2+-dependent manner. Biochemistry. PMID 28318265 DOI: 10.1021/Acs.Biochem.7B00028 |
0.332 |
|
| 2017 |
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, et al. Identification and Characterization of a Missense Mutation in the O-GlcNAc Transferase Gene that Segregates with X-Linked Intellectual Disability. The Journal of Biological Chemistry. PMID 28302723 DOI: 10.1074/Jbc.M116.771030 |
0.312 |
|
| 2017 |
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 : the Acs Journal of Surfaces and Colloids. PMID 28181811 DOI: 10.1021/Acs.Langmuir.6B04430 |
0.375 |
|
| 2017 |
Li L, Chakravorty A, Alexov E. DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. Journal of Computational Chemistry. PMID 28130775 DOI: 10.1002/Jcc.24715 |
0.37 |
|
| 2017 |
Peng Y, Alexov E. Computational investigation of proton transfer, pKa shifts and pH‐optimum of protein–DNA and protein–RNA complexes Biophysical Journal. 112: 282-295. DOI: 10.1016/J.Bpj.2016.11.2801 |
0.428 |
|
| 2016 |
Peng Y, Alexov E. Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes. Proteins. PMID 27936518 DOI: 10.1002/Prot.25221 |
0.42 |
|
| 2016 |
Peng Y, Alexov E. Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. Proteins. PMID 27696497 DOI: 10.1002/Prot.25162 |
0.395 |
|
| 2016 |
Chakavorty A, Li L, Alexov E. Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. Journal of Computational Chemistry. PMID 27546093 DOI: 10.1002/Jcc.24475 |
0.357 |
|
| 2016 |
Yang Y, Kucukkal TG, Li J, Alexov E, Cao W. Binding Analysis of Methyl-CpG Binding Domain of MeCP2 and Rett Syndrome Mutations. Acs Chemical Biology. PMID 27356039 DOI: 10.1021/Acschembio.6B00450 |
0.365 |
|
| 2016 |
Petukh M, Dai L, Alexov E. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations. International Journal of Molecular Sciences. 17: 547. PMID 27077847 DOI: 10.3390/ijms17040547 |
0.338 |
|
| 2016 |
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. International Journal of Molecular Sciences. 17: 512. PMID 27070572 DOI: 10.3390/ijms17040512 |
0.308 |
|
| 2016 |
Li L, Alper J, Alexov E. Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Scientific Reports. 6: 23249. PMID 26988596 DOI: 10.1038/Srep23249 |
0.356 |
|
| 2016 |
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. International Journal of Molecular Sciences. 17. PMID 26761001 DOI: 10.3390/Ijms17010077 |
0.397 |
|
| 2016 |
Petukh M, Dai L, Alexov E. SAAMBE: Webserver to predict the charge of binding free energy caused by amino acids mutations International Journal of Molecular Sciences. 17. DOI: 10.3390/Ijms17040547 |
0.435 |
|
| 2016 |
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 International Journal of Molecular Sciences. 17. DOI: 10.3390/Ijms17040512 |
0.419 |
|
| 2015 |
Peng Y, Alexov E. Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. Proteins. PMID 26650512 DOI: 10.1002/Prot.24968 |
0.409 |
|
| 2015 |
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. International Journal of Molecular Sciences. 16: 27270-27287. PMID 26580603 DOI: 10.3390/Ijms161126022 |
0.374 |
|
| 2015 |
Wang L, Zhang M, Alexov E. DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs. Bioinformatics (Oxford, England). PMID 26515825 DOI: 10.1093/Bioinformatics/Btv607 |
0.337 |
|
| 2015 |
Petukh M, Zhang M, Alexov E. Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence. Journal of Computational Chemistry. PMID 26484964 DOI: 10.1002/Jcc.24218 |
0.309 |
|
| 2015 |
Kucukkal T, Yang Y, Uvarov O, Cao W, Alexov E. Impact of Rett Syndrome Mutations on MeCP2 MBD Stability. Biochemistry. PMID 26418480 DOI: 10.1021/Acs.Biochem.5B00790 |
0.315 |
|
| 2015 |
Wang L, Li L, Alexov E. pKa Predictions for Proteins, RNAs and DNAs with the Gaussian Dielectric Function Using DelPhiPKa. Proteins. PMID 26408449 DOI: 10.1002/Prot.24935 |
0.405 |
|
| 2015 |
Petukh M, Li M, Alexov E. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. Plos Computational Biology. 11: e1004276. PMID 26146996 DOI: 10.1371/journal.pcbi.1004276 |
0.355 |
|
| 2015 |
Kucukkal TG, Alexov E. Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. Computational and Mathematical Methods in Medicine. 2015: 746157. PMID 26064184 DOI: 10.1155/2015/746157 |
0.413 |
|
| 2015 |
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, et al. ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons. Human Molecular Genetics. PMID 26056227 DOI: 10.1093/Hmg/Ddv208 |
0.302 |
|
| 2015 |
Li L, Wang L, Alexov E. On the energy components governing molecular recognition in the framework of continuum approaches. Frontiers in Molecular Biosciences. 2: 5. PMID 25988173 DOI: 10.3389/Fmolb.2015.00005 |
0.352 |
|
| 2015 |
Petukh M, Kucukkal TG, Alexov E. On human disease-causing amino acid variants: statistical study of sequence and structural patterns. Human Mutation. 36: 524-34. PMID 25689729 DOI: 10.1002/Humu.22770 |
0.375 |
|
| 2015 |
Kucukkal TG, Petukh M, Li L, Alexov E. Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. Current Opinion in Structural Biology. 32: 18-24. PMID 25658850 DOI: 10.1016/J.Sbi.2015.01.003 |
0.413 |
|
| 2015 |
Petukh M, Li M, Alexov E. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method Plos Computational Biology. 11. DOI: 10.1371/Journal.Pcbi.1004276 |
0.456 |
|
| 2015 |
Petukh M, Morrison J, Li M, Panchenko A, Alexov E. SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.867 |
0.455 |
|
| 2014 |
Campbell B, Petukh M, Alexov E, Li C. On the electrostatic properties of homodimeric proteins. Journal of Theoretical & Computational Chemistry. 13. PMID 25419028 DOI: 10.1142/S0219633614400070 |
0.395 |
|
| 2014 |
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. 9: e111604. PMID 25369028 DOI: 10.1371/Journal.Pone.0111604 |
0.321 |
|
| 2014 |
Kimmett T, Smith N, Witham S, Petukh M, Sarkar S, Alexov E. ProBLM web server: protein and membrane placement and orientation package. Computational and Mathematical Methods in Medicine. 2014: 838259. PMID 25126110 DOI: 10.1155/2014/838259 |
0.305 |
|
| 2014 |
Li L, Li C, Alexov E. On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function. Journal of Theoretical & Computational Chemistry. 13. PMID 25018579 DOI: 10.1142/S0219633614400021 |
0.304 |
|
| 2014 |
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. International Journal of Molecular Sciences. 15: 9670-717. PMID 24886813 DOI: 10.3390/Ijms15069670 |
0.36 |
|
| 2014 |
Li M, Petukh M, Alexov E, Panchenko AR. Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity. Journal of Chemical Theory and Computation. 10: 1770-1780. PMID 24803870 DOI: 10.1021/Ct401022C |
0.463 |
|
| 2014 |
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. Journal of Alzheimer's Disease : Jad. 39: 23-7. PMID 24121961 DOI: 10.3233/Jad-131340 |
0.301 |
|
| 2014 |
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. 9. DOI: 10.1371/Journal.Pone.0110884 |
0.385 |
|
| 2013 |
Onufriev AV, Alexov E. Protonation and pK changes in protein-ligand binding. Quarterly Reviews of Biophysics. 46: 181-209. PMID 23889892 DOI: 10.1017/S0033583513000024 |
0.353 |
|
| 2013 |
Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. Journal of Molecular Biology. 425: 3919-36. PMID 23871686 DOI: 10.1016/J.Jmb.2013.07.014 |
0.399 |
|
| 2013 |
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. 8: e66273. PMID 23799087 DOI: 10.1371/Journal.Pone.0066273 |
0.419 |
|
| 2013 |
Li C, Petukh M, Li L, Alexov E. Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi Journal of Computational Chemistry. 34: 1949-1960. PMID 23733490 DOI: 10.1002/Jcc.23340 |
0.317 |
|
| 2013 |
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. Human Molecular Genetics. 22: 3789-97. PMID 23696453 DOI: 10.1093/Hmg/Ddt229 |
0.35 |
|
| 2013 |
Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E. Enhancing human spermine synthase activity by engineered mutations. Plos Computational Biology. 9: e1002924. PMID 23468611 DOI: 10.1371/Journal.Pcbi.1002924 |
0.333 |
|
| 2013 |
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 Journal of the American Medical Informatics Association. 20: 643-651. PMID 23408511 DOI: 10.1136/Amiajnl-2012-001505 |
0.437 |
|
| 2013 |
Petukh M, Kimmet T, Alexov E. BION web server: Predicting non-specifically bound surface ions Bioinformatics. 29: 805-806. PMID 23380591 DOI: 10.1093/Bioinformatics/Btt032 |
0.324 |
|
| 2013 |
Petukh M, Stefl S, Alexov E. The role of protonation states in ligand-receptor recognition and binding Current Pharmaceutical Design. 19: 4182-4190. PMID 23170880 DOI: 10.2174/1381612811319230004 |
0.336 |
|
| 2013 |
Wang L, Zhang Z, Rocchia W, Alexov E. Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants Communications in Computational Physics. 13: 13-30. DOI: 10.4208/Cicp.300611.120911S |
0.401 |
|
| 2013 |
Wang L, Witham S, Zhang Z, Li L, Hodsdon M, Alexov E. In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor Communications in Computational Physics. 13: 207-222. DOI: 10.4208/Cicp.170911.131011S |
0.338 |
|
| 2013 |
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 Journal of Chemical Theory and Computation. 9: 2126-2136. DOI: 10.1021/Ct400065J |
0.37 |
|
| 2013 |
Li C, Petukh M, Li L, Alexov E. Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2801 |
0.344 |
|
| 2013 |
Petukh M, Li C, Alexov E. Predicting Non-Specifically Bound Ions: Application to Bion Webserver and Beryllium Disease Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2792 |
0.325 |
|
| 2013 |
Li L, Li C, Alexov E. Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.230 |
0.35 |
|
| 2013 |
Zhang Z, Pegg A, Ikeguchi Y, Alexov E. Enhancing Human Spermine Synthase Activity by Site Directed Mutations Biophysical Journal. 104: 380a. DOI: 10.1016/J.Bpj.2012.11.2117 |
0.363 |
|
| 2012 |
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 Biophysics. 5: 9. PMID 22583952 DOI: 10.1186/2046-1682-5-9 |
0.303 |
|
| 2012 |
Zhang Z, Miteva MA, Wang L, Alexov E. Analyzing effects of naturally occurring missense mutations Computational and Mathematical Methods in Medicine. 2012. PMID 22577471 DOI: 10.1155/2012/805827 |
0.404 |
|
| 2012 |
Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E. Predicting folding free energy changes upon single point mutations Bioinformatics. 28: 664-671. PMID 22238268 DOI: 10.1093/Bioinformatics/Bts005 |
0.424 |
|
| 2012 |
Petukh M, Zhenirovskyy M, Li C, Li L, Wang L, Alexov E. Predicting Nonspecific ion binding using DelPhi Biophysical Journal. 102: 2885-2893. DOI: 10.1016/J.Bpj.2012.05.013 |
0.328 |
|
| 2012 |
Witham S, Alexov E. Modeling CLIC2-RyR Interactions and the Effect of Disease Causing Mutation Biophysical Journal. 102: 4-6. DOI: 10.1016/J.Bpj.2011.11.2501 |
0.435 |
|
| 2011 |
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. 79: 3260-75. PMID 22002859 DOI: 10.1002/Prot.23189 |
0.36 |
|
| 2011 |
Witham S, Talley K, Wang L, Zhang Z, Sarkar S, Gao D, Yang W, Alexov E. Developing hybrid approaches to predict pK a values of ionizable groups Proteins: Structure, Function and Bioinformatics. 79: 3389-3399. PMID 21744395 DOI: 10.1002/Prot.23097 |
0.381 |
|
| 2011 |
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. 6: e20373. PMID 21647366 DOI: 10.1371/Journal.Pone.0020373 |
0.327 |
|
| 2011 |
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. 79: 2444-54. PMID 21630357 DOI: 10.1002/Prot.23065 |
0.387 |
|
| 2011 |
Zhang Z, Witham S, Alexov E. On the role of electrostatics in protein-protein interactions Physical Biology. 8. PMID 21572182 DOI: 10.1088/1478-3975/8/3/035001 |
0.411 |
|
| 2011 |
Mitra RC, Zhang Z, Alexov E. In silico modeling of pH-optimum of protein-protein binding. Proteins. 79: 925-36. PMID 21287623 DOI: 10.1002/Prot.22931 |
0.321 |
|
| 2011 |
Witham S, Takano K, Schwartz C, Alexov E. In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3518 |
0.38 |
|
| 2011 |
Zhang Z, Schwartz C, Alexov E. In Silico Investigation of Mutability of Spermine Synthase Biophysical Journal. 100: 321a. DOI: 10.1016/J.Bpj.2010.12.1951 |
0.357 |
|
| 2010 |
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. International Journal of Computational Biology and Drug Design. 3: 334-49. PMID 21297231 DOI: 10.1504/Ijcbdd.2010.038396 |
0.462 |
|
| 2010 |
Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E. Computational analysis of missense mutations causing Snyder-Robinson syndrome. Human Mutation. 31: 1043-9. PMID 20556796 DOI: 10.1002/Humu.21310 |
0.384 |
|
| 2010 |
Zhe Z, Shaolei T, Alexov E. In Silico Investigation of the Molecular Effects Caused by Missense Mutations in Spermine Sythase Gene Associated with Human Mental Retardation Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3099 |
0.416 |
|
| 2009 |
Teng S, Madej T, Panchenko A, Alexov E. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophysical Journal. 96: 2178-88. PMID 19289044 DOI: 10.1016/J.Bpj.2008.12.3904 |
0.446 |
|
| 2008 |
Talley K, Ng C, Shoppell M, Kundrotas PJ, Alexov E. On the electrostatic component of protein-protein binding free energy Pmc Biophysics. 1: 2-2. PMID 19351424 DOI: 10.1186/1757-5036-1-2 |
0.388 |
|
| 2008 |
Kundrotas PJ, Lensink MF, Alexov E. Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles International Journal of Biological Macromolecules. 43: 198-208. PMID 18572239 DOI: 10.1016/J.Ijbiomac.2008.05.004 |
0.383 |
|
| 2008 |
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. Current Pharmaceutical Biotechnology. 9: 123-33. PMID 18393868 DOI: 10.2174/138920108783955164 |
0.4 |
|
| 2008 |
Mitra R, Shyam R, Mitra I, Miteva MA, Alexov E. Calculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions Current Computer-Aided Drug Design. 4: 169-179. DOI: 10.2174/157340908785747393 |
0.313 |
|
| 2007 |
Miteva MA, Alexov E, Villoutreix BO. Protein structure analysis online Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. PMID 18429316 DOI: 10.1002/0471140864.Ps0213S50 |
0.382 |
|
| 2007 |
Kundrotas P, Alexov E. Predicting interacting and interfacial residues using continuous sequence segments International Journal of Biological Macromolecules. 41: 615-623. PMID 17850859 DOI: 10.1016/J.Ijbiomac.2007.08.002 |
0.362 |
|
| 2007 |
Brock K, Talley K, Coley K, Kundrotas P, Alexov E. Optimization of electrostatic interactions in protein-protein complexes Biophysical Journal. 93: 3340-3352. PMID 17693468 DOI: 10.1529/Biophysj.107.112367 |
0.387 |
|
| 2007 |
Kundrotas PJ, 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. Journal of Bioinformatics and Computational Biology. 5: 693-715. PMID 17688312 DOI: 10.1142/S0219720007002709 |
0.327 |
|
| 2007 |
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 Journal. 274: 3363-3373. PMID 17542990 DOI: 10.1111/J.1742-4658.2007.05870.X |
0.3 |
|
| 2007 |
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 International Journal of Biological Macromolecules. 41: 114-119. PMID 17320167 DOI: 10.1016/J.Ijbiomac.2007.01.007 |
0.309 |
|
| 2007 |
Isvoran A, Craescu CT, Alexov E. Electrostatic control of the overall shape of calmodulin: Numerical calculations European Biophysics Journal. 36: 225-237. PMID 17285296 DOI: 10.1007/S00249-006-0123-1 |
0.303 |
|
| 2007 |
Tang CL, Alexov E, Pyle AM, Honig B. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of Molecular Biology. 366: 1475-96. PMID 17223134 DOI: 10.1016/J.Jmb.2006.12.001 |
0.302 |
|
| 2007 |
Bertonati C, Honig B, Alexov E. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophysical Journal. 92: 1891-9. PMID 17208980 DOI: 10.1529/Biophysj.106.092122 |
0.416 |
|
| 2007 |
Kundrotas PJ, Alexov E. PROTCOM: Searchable database of protein complexes enhanced with domain-domain structures Nucleic Acids Research. 35. PMID 17071962 DOI: 10.1093/Nar/Gkl768 |
0.351 |
|
| 2006 |
Kundrotas PJ, Alexov E. Predicting 3D structures of transient protein-protein complexes by homology Biochimica Et Biophysica Acta - Proteins and Proteomics. 1764: 1498-1511. PMID 16963323 DOI: 10.1016/J.Bbapap.2006.08.002 |
0.358 |
|
| 2006 |
Kundrotas PJ, Alexov E. Electrostatic properties of protein-protein complexes Biophysical Journal. 91: 1724-1736. PMID 16782791 DOI: 10.1529/Biophysj.106.086025 |
0.359 |
|
| 2006 |
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. Journal of Molecular Biology. 355: 1078-94. PMID 16332376 DOI: 10.1016/J.Jmb.2005.11.001 |
0.322 |
|
| 2005 |
Zhu J, Alexov E, Honig B. Comparative study of generalized born models: Born radii and peptide folding. The Journal of Physical Chemistry. B. 109: 3008-22. PMID 16851315 DOI: 10.1021/Jp046307S |
0.301 |
|
| 2005 |
Shosheva A, Donchev A, Dimitrov M, Kostov G, Toromanov G, Getov V, Alexov E. Comparative study of the stability of poplar plastocyanin isoforms Biochimica Et Biophysica Acta - Proteins and Proteomics. 1748: 116-127. PMID 15752700 DOI: 10.1016/J.Bbapap.2004.12.012 |
0.301 |
|
| 2004 |
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: Structure, Function and Genetics. 56: 572-584. PMID 15229889 DOI: 10.1002/Prot.20107 |
0.396 |
|
| 2004 |
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 Biochimica Et Biophysica Acta - Proteins and Proteomics. 1698: 67-75. PMID 15063316 DOI: 10.1016/J.Bbapap.2003.10.010 |
0.318 |
|
| 2004 |
Alexov E. Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure European Journal of Biochemistry. 271: 173-185. PMID 14686930 DOI: 10.1046/J.1432-1033.2003.03917.X |
0.318 |
|
| 2003 |
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. 53: 430-5. PMID 14579332 DOI: 10.1002/Prot.10550 |
0.333 |
|
| 2003 |
Alexov E. Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: Comparing experimental with computed pKas Proteins: Structure, Function and Genetics. 50: 94-103. PMID 12471602 DOI: 10.1002/Prot.10265 |
0.356 |
|
| 2002 |
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. Journal of Computational Chemistry. 23: 128-37. PMID 11913378 DOI: 10.1002/Jcc.1161 |
0.313 |
|
| 2001 |
Tandori J, Baciou L, Alexov E, Maróti 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 Journal of Biological Chemistry. 276: 45513-45515. PMID 11604387 DOI: 10.1074/Jbc.C100537200 |
0.317 |
|
| 2000 |
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 Q(A)- to Q(B) in photosynthetic reaction centers Biochemistry. 39: 5940-5952. PMID 10821665 DOI: 10.1021/Bi9929498 |
0.324 |
|
| 2000 |
Gunner MR, Alexov E. A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins Biochimica Et Biophysica Acta - Bioenergetics. 1458: 63-87. PMID 10812025 DOI: 10.1016/S0005-2728(00)00060-8 |
0.349 |
|
| 1998 |
Miteva M, Alexov E, Atanasov B. Numerical simulation of aldolase tetramer stability European Biophysics Journal. 28: 67-73. DOI: 10.1007/S002490050184 |
0.36 |
|
| 1997 |
Gunner MR, Alexov E, Torres E, Lipovaca S. The importance of the protein in controlling the electrochemistry of heme metalloproteins: Methods of calculation and analysis Journal of Biological Inorganic Chemistry. 2: 126-134. DOI: 10.1007/S007750050116 |
0.378 |
|
| Show low-probability matches. |