@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{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" } @inproceedings{chakravorty2019effect, author = "A. Chakravorty and J. Higham and E. Alexov and R. Henchman", title = "Effect of water on the entropy of protein-protein binding", year = 2019, booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY", volume = 258 } @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{shashikala2019modeling, author = "H. Shashikala and A. Chakravorty and E. Alexov", title = "Modeling electrostatic force in protein-protein recognition", year = 2019, journal = "Frontiers in molecular biosciences", publisher = "Frontiers", volume = 6, pages = "94" } @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" } @article{bosthanthirige2019modeling, author = "M. S. H. Bosthanthirige and A. Chakravorty and E. Alexov", title = "Modeling Electrostatic Force in Protein-Protein Recognition", year = 2019, journal = "Biophysical Journal", publisher = "Elsevier", volume = 116, number = 3, pages = "46a" } @article{chakravorty2019new, author = "A. Chakravorty and J. Higham and E. Alexov and R. H. Henchman", title = "New method to determine the effect of dimerization on protein flexibility from molecular dynamics simulation using structural hierarchy", year = 2019, journal = "Biophysical Journal", publisher = "Elsevier", volume = 116, number = 3, pages = "561a-562a" } @article{chakravorty2019grid, author = "A. Chakravorty and E. Gallicchio and E. Alexov", title = "A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry", year = 2019, journal = "Journal of computational chemistry", publisher = "John Wiley \& Sons, Inc. Hoboken, USA", volume = 40, number = 12, pages = "1290-1304" } @article{chakravorty2018gaussian, author = "A. Chakravorty and Z. Jia and Y. Peng and N. Tajielyato and L. Wang and E. Alexov", title = "Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents", year = 2018, journal = "Frontiers in molecular biosciences", publisher = "Frontiers", volume = 5, pages = "25" } @article{chakravorty2018reproducing, author = "A. Chakravorty and Z. Jia and L. Li and S. Zhao and E. Alexov", title = "Reproducing the ensemble average polar solvation energy of a protein from a single structure: gaussian-based smooth dielectric function for macromolecular modeling", year = 2018, journal = "Journal of chemical theory and computation", publisher = "American Chemical Society", volume = 14, number = 2, pages = "1020-1032" } @article{li2017delphiforce, author = "L. Li and Z. Jia and Y. Peng and A. Chakravorty and L. Sun and E. Alexov", title = "DelPhiForce web server: electrostatic forces and energy calculations and visualization", year = 2017, journal = "Bioinformatics", publisher = "Oxford University Press", volume = 33, number = 22, pages = "3661-3663" } @patent{jia2017treating, author = "Z. Jia and L. Li and A. Chakravorty and E. Alexov", title = "Treating ion distribution with G aussian-based smooth dielectric function in DelPhi", year = 2017 } @article{chakravorty2017new, author = "A. Chakravorty and Z. Jia and L. Li and E. Alexov", title = "A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential", year = 2017, journal = "Langmuir", publisher = "American Chemical Society", volume = 33, number = 9, pages = "2283-2295" } @article{li2017delphiforce, author = "L. Li and A. Chakravorty and E. Alexov", title = "DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding", year = 2017, journal = "Journal of computational chemistry", volume = 38, number = 9, pages = "584-593" }