@article{Shapovalov2025,
  author = "I. Shapovalov and P. Rimal and P. Poudel and V. Lewtas and M. Bell and S. K. Panday and B. J. Laight and D. Harper and S. Grieve and G. S. Baillie and K. Nouri and P. L. Davies and E. Alexov and P. A. Greer",
  title = "Quantification and structure-function analysis of calpain-1 and calpain-2 protease subunit interactions",
  year = 2025,
  journal = "Journal of Biological Chemistry",
  publisher = "Elsevier BV",
  pages = "110243",
  month = "May",
  doi = "10.1016/j.jbc.2025.110243",
  url = "http://dx.doi.org/10.1016/j.jbc.2025.110243"
}


@article{Poudel2025,
  author = "P. Poudel and I. Shapovalov and S. K. Panday and K. Nouri and P. L. Davies and P. A. Greer and E. Alexov",
  title = "In Silico Screening for Small Molecules to Alter Calpain Proteolysis through Modulating Conformation Changes Induced by Heterodimerization",
  year = 2025,
  journal = "Journal of Chemical Information and Modeling",
  publisher = "American Chemical Society (ACS)",
  month = "May",
  doi = "10.1021/acs.jcim.5c00258",
  url = "http://dx.doi.org/10.1021/acs.jcim.5c00258"
}


@article{Chen2025,
  author = "A. Y. Chen and S. K. Panday and K. Ri and E. Alexov and B. R. Brooks and A. Damjanovic",
  title = "PKAD-R: Curated, Redesigned and Expanded Database of Experimental pKa Values in Proteins",
  year = 2025,
  journal = "Journal of Computational Biophysics and Chemistry",
  publisher = "World Scientific Pub Co Pte Ltd",
  pages = "1–15",
  month = "Apr",
  doi = "10.1142/s2737416525500164",
  url = "http://dx.doi.org/10.1142/S2737416525500164"
}


@article{Turina2025,
  author = "P. Turina and M. Petrosino and C. A. E. Sandoval and L. Novak and A. Pasquo and E. Alexov and M. A. Alladin and D. B. Ascher and G. Babbi and C. Bakolitsa and R. Casadio and J. Cheng and P. Fariselli and L. Folkman and A. Kamandula and P. Katsonis and M. Li and D. Li and O. Lichtarge and S. Mahmud and P. L. Martelli and D. Pal and S. K. Panday and D. E. V. Pires and S. Portelli and F. Pucci and C. H. M. Rodrigues and M. Rooman and C. Savojardo and M. Schwersensky and Y. Shen and A. V. Strokach and Y. Sun and J. Woo and P. Radivojac and S. E. Brenner and R. Chiaraluce and V. Consalvi and E. Capriotti",
  title = "Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges",
  year = 2025,
  journal = "Human Genetics",
  publisher = "Springer Science and Business Media LLC",
  volume = 144,
  number = 23,
  pages = "265–280",
  month = "Feb",
  doi = "10.1007/s00439-024-02724-8",
  url = "http://dx.doi.org/10.1007/s00439-024-02724-8"
}


@article{Rimal2025,
  author = "P. Rimal and S. Paul and S. Panday and E. Alexov",
  title = "Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA",
  year = 2025,
  journal = "Genes",
  publisher = "MDPI AG",
  volume = 16,
  number = 1,
  pages = "101",
  month = "Jan",
  doi = "10.3390/genes16010101",
  url = "http://dx.doi.org/10.3390/genes16010101"
}


@article{Turina2024,
  author = "P. Turina and G. D. Cortivo and C. A. E. Sandoval and E. Alexov and D. B. Ascher and G. Babbi and C. Bakolitsa and R. Casadio and P. Fariselli and L. Folkman and A. Kamandula and P. Katsonis and D. Li and O. Lichtarge and P. L. Martelli and S. K. Panday and D. E. V. Pires and S. Portelli and F. Pucci and C. H. M. Rodrigues and M. Rooman and C. Savojardo and M. Schwersensky and Y. Shen and A. V. Strokach and Y. Sun and J. Woo and P. Radivojac and S. E. Brenner and D. Dell’Orco and E. Capriotti",
  title = "Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges",
  year = 2024,
  journal = "Human Genetics",
  publisher = "Springer Science and Business Media LLC",
  volume = 144,
  number = 23,
  pages = "113–125",
  month = "Dec",
  doi = "10.1007/s00439-024-02720-y",
  url = "http://dx.doi.org/10.1007/s00439-024-02720-y"
}


@article{Panday2024,
  author = "S. K. Panday and V. Shankar and R. A. Lyman and E. Alexov",
  title = "Genetic Variants Linked to Opioid Addiction: A Genome-Wide Association Study",
  year = 2024,
  journal = "International Journal of Molecular Sciences",
  publisher = "MDPI AG",
  volume = 25,
  number = 23,
  pages = "12516",
  month = "Nov",
  doi = "10.3390/ijms252312516",
  url = "http://dx.doi.org/10.3390/ijms252312516"
}


@article{Panday2024,
  author = "S. K. Panday and A. Chakravorty and S. Zhao and E. Alexov",
  title = "On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super‐Gaussian Poisson–Boltzmann model",
  year = 2024,
  journal = "Journal of Computational Chemistry",
  publisher = "Wiley",
  volume = 46,
  number = 1,
  month = "Oct",
  doi = "10.1002/jcc.27496",
  url = "http://dx.doi.org/10.1002/jcc.27496"
}


@article{Rimal2024,
  author = "P. Rimal and S. K. Panday and W. Xu and Y. Peng and E. Alexov",
  title = "SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes",
  year = 2024,
  journal = "Bioinformatics",
  publisher = "Oxford University Press (OUP)",
  volume = 40,
  number = 9,
  month = "Sep",
  doi = "10.1093/bioinformatics/btae544",
  url = "http://dx.doi.org/10.1093/bioinformatics/btae544"
}


@article{Pandey2023,
  author = "P. Pandey and S. K. Panday and P. Rimal and N. Ancona and E. Alexov",
  title = "Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations",
  year = 2023,
  journal = "International Journal of Molecular Sciences",
  publisher = "MDPI AG",
  volume = 24,
  number = 15,
  pages = "12073",
  month = "Jul",
  doi = "10.3390/ijms241512073",
  url = "http://dx.doi.org/10.3390/ijms241512073"
}


@article{Panday2022a,
  author = "S. Panday and E. Alexov",
  title = "Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation",
  year = 2022,
  journal = "ACS omega",
  volume = 7,
  number = 13,
  pages = "11057-11067"
}


@article{li2021sampdi,
  author = "G. Li and S. Panday and Y. Peng and E. Alexov",
  title = "SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.",
  year = 2021,
  journal = "Bioinformatics (Oxford, England)"
}


@article{li2021saafec,
  author = "G. Li and S. K. Panday and E. Alexov",
  title = "SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability",
  year = 2021,
  journal = "International Journal of Molecular Sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 22,
  number = 2,
  pages = "606"
}


@article{shashikala2021bion,
  author = "H. Shashikala and A. Chakravorty and S. K. Panday and E. Alexov",
  title = "BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics",
  year = 2021,
  journal = "International Journal of Molecular Sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 22,
  number = 1,
  pages = "272"
}


@article{Li2021c,
  author = "G. Li and S. Panday and Y. Peng and E. Alexov",
  title = "SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions",
  year = 2021,
  journal = "Bioinformatics",
  volume = 37,
  number = 21,
  pages = "3760-3765"
}


@article{chakravorty2020capturing,
  author = "A. Chakravorty and S. Panday and S. Pahari and S. Zhao and E. Alexov",
  title = "Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi",
  year = 2020,
  journal = "Journal of chemical information and modeling",
  publisher = "American Chemical Society",
  volume = 60,
  number = 4,
  pages = "2229-2246"
}


@article{panday2019reproducing,
  author = "S. K. Panday and M. H. Shashikala and A. Chakravorty and S. Zhao and E. Alexov",
  title = "Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes",
  year = 2019,
  journal = "Communications in Information and Systems",
  volume = 19,
  number = 4
}


@article{panday2019modeling,
  author = "S. K. Panday and M. H. Shashikala and M. Koirala and S. Pahari and A. Chakvorty and Y. Peng and L. Li and Z. Jia and C. Li and E. Alexov",
  title = "Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]",
  year = 2019,
  journal = "Living Journal of Computational Molecular Science",
  publisher = "University of Colorado Boulder",
  volume = 1,
  number = 2,
  pages = "10841"
}


@article{li2019delphi,
  author = "C. Li and Z. Jia and A. Chakravorty and S. Pahari and Y. Peng and S. Basu and M. Koirala and S. K. Panday and M. Petukh and L. Li and others",
  title = "DelPhi suite: New developments and review of functionalities",
  year = 2019,
  journal = "Journal of computational chemistry",
  publisher = "John Wiley \& Sons, Inc. Hoboken, USA",
  volume = 40,
  number = 28,
  pages = "2502-2508"
}