I. Shapovalov, P. Rimal, P. Poudel, V. Lewtas, M. Bell, S. K. Panday, B. J. Laight, D. Harper, S. Grieve, G. S. Baillie, K. Nouri, P. L. Davies, E. Alexov, and P. A. Greer. Quantification and structure-function analysis of calpain-1 and calpain-2 protease subunit interactions. Journal of Biological Chemistry, Elsevier BV, pages 110243, May 2025.

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, American Chemical Society (ACS), May 2025.

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, World Scientific Pub Co Pte Ltd, pages 1–15, April 2025.

P. Turina, M. Petrosino, C. A. E. Sandoval, L. Novak, A. Pasquo, E. Alexov, M. A. Alladin, D. B. Ascher, G. Babbi, C. Bakolitsa, R. Casadio, J. Cheng, P. Fariselli, L. Folkman, A. Kamandula, P. Katsonis, M. Li, D. Li, O. Lichtarge, S. Mahmud, P. L. Martelli, D. Pal, S. K. Panday, D. E. V. Pires, S. Portelli, F. Pucci, C. H. M. Rodrigues, M. Rooman, C. Savojardo, M. Schwersensky, Y. Shen, A. V. Strokach, Y. Sun, J. Woo, P. Radivojac, S. E. Brenner, R. Chiaraluce, V. Consalvi, and E. Capriotti. Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges. Human Genetics, Springer Science and Business Media LLC, volume 144, issue 23, pages 265–280, February 2025.

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, MDPI AG, volume 16, issue 1, pages 101, January 2025.

P. Turina, G. D. Cortivo, C. A. E. Sandoval, E. Alexov, D. B. Ascher, G. Babbi, C. Bakolitsa, R. Casadio, P. Fariselli, L. Folkman, A. Kamandula, P. Katsonis, D. Li, O. Lichtarge, P. L. Martelli, S. K. Panday, D. E. V. Pires, S. Portelli, F. Pucci, C. H. M. Rodrigues, M. Rooman, C. Savojardo, M. Schwersensky, Y. Shen, A. V. Strokach, Y. Sun, J. Woo, P. Radivojac, S. E. Brenner, D. Dell’Orco, and E. Capriotti. Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges. Human Genetics, Springer Science and Business Media LLC, volume 144, issue 23, pages 113–125, December 2024.

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, MDPI AG, volume 25, issue 23, pages 12516, November 2024.

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, Wiley, volume 46, issue 1, October 2024.

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, Oxford University Press (OUP), volume 40, issue 9, September 2024.

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, MDPI AG, volume 24, issue 15, pages 12073, July 2023.

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, volume 7, issue 13, pages 11057-11067, 2022.

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.

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, Multidisciplinary Digital Publishing Institute, volume 22, issue 2, pages 606, 2021.

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, Multidisciplinary Digital Publishing Institute, volume 22, issue 1, pages 272, 2021.

G. Li, S. Panday, Y. Peng, and E. Alexov. SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions. Bioinformatics, volume 37, issue 21, pages 3760-3765, 2021.

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, American Chemical Society, volume 60, issue 4, pages 2229-2246, 2020.

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, volume 19, issue 4, 2019.

S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, C. Li, and E. Alexov. Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]. Living Journal of Computational Molecular Science, University of Colorado Boulder, volume 1, issue 2, pages 10841, 2019.

C. Li, Z. Jia, A. Chakravorty, S. Pahari, Y. Peng, S. Basu, M. Koirala, S. K. Panday, M. Petukh, L. Li, and others. DelPhi suite: New developments and review of functionalities. Journal of computational chemistry, John Wiley \& Sons, Inc. Hoboken, USA, volume 40, issue 28, pages 2502-2508, 2019.