Computational Biophysics and Bioinformatics

C. Li, Z. Jia, A. Chakravorty, S. Pahari, Y. Peng, S. Basu, M. Koirala, S. K. Panday, et al.
DelPhi suite: New developments and review of functionalities
Journal of computational chemistry, 40(28), 2502-2508, 2019
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M. Petukh, L. Dai, and E. Alexov
SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations
International journal of molecular sciences, 17(4), 547, 2016
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I. Getov, M. Petukh, and E. Alexov
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(4), 512, 2016
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M. Petukh, J. Morrison, M. Li, A. Panchenko, and E. Alexov
SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy
Biophysical Journal, 108(2), 157a-158a, 2015
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M. Petukh, M. Zhang, and E. Alexov
Statistical investigation of surface bound ions and further development of BION server to include p H and salt dependence
Journal of computational chemistry, 36(32), 2381-2393, 2015
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M. Petukh, M. Li, and E. Alexov
Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method
PLoS computational biology, 11(7), e1004276, 2015
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M. Petukh, T. G. Kucukkal, and E. Alexov
On human disease-causing amino acid variants: Statistical study of sequence and structural patterns
Human mutation, 36(5), 524-534, 2015
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T. G. Kucukkal, M. Petukh, L. Li, and E. Alexov
Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins
Current opinion in structural biology, 32, 18-24, 2015
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B. Campbell, M. Petukh, E. Alexov, and C. Li
On the electrostatic properties of homodimeric proteins
Journal of Theoretical and Computational Chemistry, 13(3), 1440007, 2014
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M. Petukh and E. Alexov
Ion binding to biological macromolecules
Asian journal of physics: an international quarterly research journal, 23(5), 735, 2014
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M. Petukh, B. Wu, S. Stefl, N. Smith, D. Hyde-Volpe, L. Wang, and E. Alexov
Chronic beryllium disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2
PLoS One, 9(11), e111604, 2014
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T. Kimmett, N. Smith, S. Witham, M. Petukh, S. Sarkar, and E. Alexov
ProBLM web server: protein and membrane placement and orientation package
Computational and mathematical methods in medicine, 2014, 2014
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M. Li, M. Petukh, E. Alexov, and A. R. Panchenko
Predicting the impact of missense mutations on protein--protein binding affinity
Journal of chemical theory and computation, 10(4), 1770-1780, 2014
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L. Boccuto, K. Aoki, H. Flanagan-Steet, C.-F. Chen, X. Fan, F. Bartel, M. Petukh, A. Pittman, et al.
A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt \& pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation
Human molecular genetics, 23(2), 418-433, 2014
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C. Li, M. Petukh, L. Li, and E. Alexov
Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi
Biophysical Journal, 104(2), 507a, 2013
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M. Petukh, C. Li, and E. Alexov
Predicting non-specifically bound ions: Application to BION webserver and beryllium disease
Biophysical Journal, 104(2), 506a, 2013
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M. Petukh, T. Kimmet, and E. Alexov
BION web server: predicting non-specifically bound surface ions
Bioinformatics, 29(6), 805-806, 2013
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C. Li, M. Petukh, L. Li, and E. Alexov
Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi
Journal of computational chemistry, 34(22), 1949-1960, 2013
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Z. Zhang, S. Witham, M. Petukh, G. Moroy, M. Miteva, Y. Ikeguchi, and E. Alexov
A rational free energy-based approach to understanding and targeting disease-causing missense mutations
Journal of the American Medical Informatics Association, 20(4), 643-651, 2013
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Z. Zhang, Y. Zheng, M. Petukh, A. Pegg, Y. Ikeguchi, and E. Alexov
Enhancing human spermine synthase activity by engineered mutations
PLoS Comput Biol, 9(2), e1002924, 2013
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C. Li, L. Li, M. Petukh, and E. Alexov
Progress in developing Poisson-Boltzmann equation solvers
Computational and Mathematical Biophysics, 1(1), 42-62, 2013
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M. Petukh, S. Stefl, and E. Alexov
The role of protonation states in ligand-receptor recognition and binding
Current pharmaceutical design, 19(23), 4182-4190, 2013
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S. Stefl, H. Nishi, M. Petukh, A. R. Panchenko, and E. Alexov
Molecular mechanisms of disease-causing missense mutations
Journal of molecular biology, 425(21), 3919-3936, 2013
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M. Petukh, M. Zhenirovskyy, C. Li, L. Li, L. Wang, and E. Alexov
Predicting nonspecific ion binding using DelPhi
Biophysical journal, 102(12), 2885-2893, 2012
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L. Li, C. Li, S. Sarkar, J. Zhang, S. Witham, Z. Zhang, L. Wang, N. Smith, et al.
DelPhi: a comprehensive suite for DelPhi software and associated resources
BMC biophysics, 5(1), 1-11, 2012
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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

Journal Articles by M. Petukh

Conference Papers