TY - JOUR T1 - DelPhi suite: New developments and review of functionalities AU - Li, C. AU - Jia, Z. AU - Chakravorty, A. AU - Pahari, S. AU - Peng, Y. AU - Basu, S. AU - Koirala, M. AU - Panday, S. K. AU - Petukh, M. AU - Li, L. AU - others, JO - Journal of computational chemistry PY - 2019 PB - John Wiley \& Sons, Inc. Hoboken, USA VL - 40 IS - 28 SP - 2502 EP - 2508 ER - TY - JOUR T1 - SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations AU - Petukh, M. AU - Dai, L. AU - Alexov, E. JO - International journal of molecular sciences PY - 2016 PB - Multidisciplinary Digital Publishing Institute VL - 17 IS - 4 SP - 547 EP - 547 ER - TY - JOUR T1 - SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach AU - Getov, I. AU - Petukh, M. AU - Alexov, E. JO - International journal of molecular sciences PY - 2016 PB - Multidisciplinary Digital Publishing Institute VL - 17 IS - 4 SP - 512 EP - 512 ER - TY - CHAP T1 - Predicting folding free energy changes caused by single point mutations via combined usage of MM-PBSA method and biophysical characteristics AU - Getov, I. AU - Petukh, M. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2015 VL - 250 ER - TY - JOUR T1 - SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy AU - Petukh, M. AU - Morrison, J. AU - Li, M. AU - Panchenko, A. AU - Alexov, E. JO - Biophysical Journal PY - 2015 PB - Elsevier VL - 108 IS - 2 SP - 157a EP - 158a ER - TY - JOUR T1 - Statistical investigation of surface bound ions and further development of BION server to include p H and salt dependence AU - Petukh, M. AU - Zhang, M. AU - Alexov, E. JO - Journal of computational chemistry PY - 2015 VL - 36 IS - 32 SP - 2381 EP - 2393 ER - TY - JOUR T1 - Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method AU - Petukh, M. AU - Li, M. AU - Alexov, E. JO - PLoS computational biology PY - 2015 PB - Public Library of Science San Francisco, CA USA VL - 11 IS - 7 SP - e1004276 EP - e1004276 ER - TY - JOUR T1 - On human disease-causing amino acid variants: Statistical study of sequence and structural patterns AU - Petukh, M. AU - Kucukkal, T. G. AU - Alexov, E. JO - Human mutation PY - 2015 VL - 36 IS - 5 SP - 524 EP - 534 ER - TY - JOUR T1 - Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins AU - Kucukkal, T. G. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Current opinion in structural biology PY - 2015 PB - Elsevier Current Trends VL - 32 SP - 18 EP - 24 ER - TY - JOUR T1 - On the electrostatic properties of homodimeric proteins AU - Campbell, B. AU - Petukh, M. AU - Alexov, E. AU - Li, C. JO - Journal of Theoretical and Computational Chemistry PY - 2014 PB - World Scientific Publishing Company VL - 13 IS - 3 SP - 1440007 EP - 1440007 ER - TY - JOUR T1 - Ion binding to biological macromolecules AU - Petukh, M. AU - Alexov, E. JO - Asian journal of physics: an international quarterly research journal PY - 2014 PB - NIH Public Access VL - 23 IS - 5 SP - 735 EP - 735 ER - TY - JOUR T1 - Chronic beryllium disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2 AU - Petukh, M. AU - Wu, B. AU - Stefl, S. AU - Smith, N. AU - Hyde-Volpe, D. AU - Wang, L. AU - Alexov, E. JO - PLoS One PY - 2014 PB - Public Library of Science VL - 9 IS - 11 SP - e111604 EP - e111604 ER - TY - JOUR T1 - ProBLM web server: protein and membrane placement and orientation package AU - Kimmett, T. AU - Smith, N. AU - Witham, S. AU - Petukh, M. AU - Sarkar, S. AU - Alexov, E. JO - Computational and mathematical methods in medicine PY - 2014 PB - Hindawi VL - 2014 ER - TY - JOUR T1 - Predicting the impact of missense mutations on protein--protein binding affinity AU - Li, M. AU - Petukh, M. AU - Alexov, E. AU - Panchenko, A. R. JO - Journal of chemical theory and computation PY - 2014 PB - American Chemical Society VL - 10 IS - 4 SP - 1770 EP - 1780 ER - TY - JOUR T1 - A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt \& pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation AU - Boccuto, L. AU - Aoki, K. AU - Flanagan-Steet, H. AU - Chen, C.-F. AU - Fan, X. AU - Bartel, F. AU - Petukh, M. AU - Pittman, A. AU - Saul, R. AU - Chaubey, A. AU - others, JO - Human molecular genetics PY - 2014 PB - Oxford University Press VL - 23 IS - 2 SP - 418 EP - 433 ER - TY - CHAP T1 - Electrostatics plays significant role in changes of the protein-protein affinity due to missense mutations AU - Petukh, M. AU - Panchenko, A. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2013 VL - 246 ER - TY - JOUR T1 - Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi AU - Li, C. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 507a EP - 507a ER - TY - JOUR T1 - Predicting non-specifically bound ions: Application to BION webserver and beryllium disease AU - Petukh, M. AU - Li, C. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 506a EP - 506a ER - TY - JOUR T1 - BION web server: predicting non-specifically bound surface ions AU - Petukh, M. AU - Kimmet, T. AU - Alexov, E. JO - Bioinformatics PY - 2013 PB - Oxford University Press VL - 29 IS - 6 SP - 805 EP - 806 ER - TY - JOUR T1 - Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi AU - Li, C. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Journal of computational chemistry PY - 2013 PB - Wiley Online Library VL - 34 IS - 22 SP - 1949 EP - 1960 ER - TY - JOUR T1 - A rational free energy-based approach to understanding and targeting disease-causing missense mutations AU - Zhang, Z. AU - Witham, S. AU - Petukh, M. AU - Moroy, G. AU - Miteva, M. AU - Ikeguchi, Y. AU - Alexov, E. JO - Journal of the American Medical Informatics Association PY - 2013 PB - BMJ Publishing Group BMA House, Tavistock Square, London, WC1H 9JR VL - 20 IS - 4 SP - 643 EP - 651 ER - TY - JOUR T1 - Enhancing human spermine synthase activity by engineered mutations AU - Zhang, Z. AU - Zheng, Y. AU - Petukh, M. AU - Pegg, A. AU - Ikeguchi, Y. AU - Alexov, E. JO - PLoS Comput Biol PY - 2013 PB - Public Library of Science VL - 9 IS - 2 SP - e1002924 EP - e1002924 ER - TY - JOUR T1 - Progress in developing Poisson-Boltzmann equation solvers AU - Li, C. AU - Li, L. AU - Petukh, M. AU - Alexov, E. JO - Computational and Mathematical Biophysics PY - 2013 PB - De Gruyter VL - 1 IS - 1 SP - 42 EP - 62 ER - TY - JOUR T1 - The role of protonation states in ligand-receptor recognition and binding AU - Petukh, M. AU - Stefl, S. AU - Alexov, E. JO - Current pharmaceutical design PY - 2013 PB - Bentham Science Publishers VL - 19 IS - 23 SP - 4182 EP - 4190 ER - TY - JOUR T1 - Molecular mechanisms of disease-causing missense mutations AU - Stefl, S. AU - Nishi, H. AU - Petukh, M. AU - Panchenko, A. R. AU - Alexov, E. JO - Journal of molecular biology PY - 2013 PB - Academic Press VL - 425 IS - 21 SP - 3919 EP - 3936 ER - TY - JOUR T1 - Predicting nonspecific ion binding using DelPhi AU - Petukh, M. AU - Zhenirovskyy, M. AU - Li, C. AU - Li, L. AU - Wang, L. AU - Alexov, E. JO - Biophysical journal PY - 2012 PB - Elsevier VL - 102 IS - 12 SP - 2885 EP - 2893 ER - TY - JOUR T1 - DelPhi: a comprehensive suite for DelPhi software and associated resources AU - Li, L. AU - Li, C. AU - Sarkar, S. AU - Zhang, J. AU - Witham, S. AU - Zhang, Z. AU - Wang, L. AU - Smith, N. AU - Petukh, M. AU - Alexov, E. JO - BMC biophysics PY - 2012 PB - BioMed Central VL - 5 IS - 1 SP - 1 EP - 11 ER -