Computational Biophysics and Bioinformatics

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. K. Panday