Computational Biophysics and Bioinformatics

I. Shapovalov, P. Rimal, P. Poudel, V. Lewtas, M. Bell, S. K. Panday, B. J. Laight, D. Harper, et al.
Quantification and structure-function analysis of calpain-1 and calpain-2 protease subunit interactions
Journal of Biological Chemistry, 110243, 2025
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P. Poudel, I. Shapovalov, S. K. Panday, K. Nouri, P. L. Davies, P. A. Greer, and E. Alexov
In Silico Screening for Small Molecules to Alter Calpain Proteolysis through Modulating Conformation Changes Induced by Heterodimerization
Journal of Chemical Information and Modeling, 2025
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A. Y. Chen, S. K. Panday, K. Ri, E. Alexov, B. R. Brooks, and A. Damjanovic
PKAD-R: Curated, Redesigned and Expanded Database of Experimental pKa Values in Proteins
Journal of Computational Biophysics and Chemistry, 1–15, 2025
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P. Turina, M. Petrosino, C. A. E. Sandoval, L. Novak, A. Pasquo, E. Alexov, M. A. Alladin, D. B. Ascher, et al.
Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges
Human Genetics, 144(23), 265–280, 2025
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P. Rimal, S. Paul, S. Panday, and E. Alexov
Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA
Genes, 16(1), 101, 2025
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P. Turina, G. D. Cortivo, C. A. E. Sandoval, E. Alexov, D. B. Ascher, G. Babbi, C. Bakolitsa, R. Casadio, et al.
Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges
Human Genetics, 144(23), 113–125, 2024
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S. K. Panday, V. Shankar, R. A. Lyman, and E. Alexov
Genetic Variants Linked to Opioid Addiction: A Genome-Wide Association Study
International Journal of Molecular Sciences, 25(23), 12516, 2024
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S. K. Panday, A. Chakravorty, S. Zhao, and E. Alexov
On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super‐Gaussian Poisson–Boltzmann model
Journal of Computational Chemistry, 46(1), 2024
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P. Rimal, S. K. Panday, W. Xu, Y. Peng, and E. Alexov
SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes
Bioinformatics, 40(9), 2024
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P. Pandey, S. K. Panday, P. Rimal, N. Ancona, and E. Alexov
Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations
International Journal of Molecular Sciences, 24(15), 12073, 2023
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S. Panday and E. Alexov
Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation
ACS omega, 7(13), 11057-11067, 2022
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G. Li, S. Panday, Y. Peng, and E. Alexov
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.
Bioinformatics (Oxford, England), 2021
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G. Li, S. K. Panday, and 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, 2021
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H. Shashikala, A. Chakravorty, S. K. Panday, and 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, 2021
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G. Li, S. Panday, Y. Peng, and E. Alexov
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions
Bioinformatics, 37(21), 3760-3765, 2021
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A. Chakravorty, S. Panday, S. Pahari, S. Zhao, and 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, 60(4), 2229-2246, 2020
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S. K. Panday, M. H. Shashikala, A. Chakravorty, S. Zhao, and E. Alexov
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(4), 2019
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S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, et al.
Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]
Living Journal of Computational Molecular Science, 1(2), 10841, 2019
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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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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

Journal Articles by S. Panday