Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. - Walter Rocchia; Sundaram Sridharan; Anthony Nicholls; Emil Alexov; Alessandro Chiabrera; Barry Honig (J. Comput. Chem., 2002)

Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. - Petras J. Kundrotas; Emil Alexov (BMC Bioinform., 2006)

Assessing the Quality of the Homology-Modeled 3D Structures from electrostatic Standpoint: Test on bacterial nucleoside monophosphate kinase Families. - Petras J. Kundrotas; Paulina Georgieva; Alexandra Shosheva; Petya Christova; Emil Alexov (J. Bioinform. Comput. Biol., 2007)

PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. - Petras J. Kundrotas; Emil Alexov (Nucleic Acids Res., 2007)

Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interaction. - Shaolei Teng; Anand K. Srivastava; Charles E. Schwartz; Emil Alexov; Liangjiang Wang (Int. J. Comput. Biol. Drug Des., 2010)

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. - Nicholas Smith; Shawn Witham; Subhra Sarkar; Jie Zhang 035; Lin Li 003; Chuan Li 003; Emil Alexov (Bioinform., 2012)

Predicting folding free energy changes upon single point mutations. - Zhe Zhang; Lin Wang; Yang Gao; Jie Zhang 035; Maxim Zhenirovskyy; Emil Alexov (Bioinform., 2012)

Analyzing Effects of Naturally Occurring Missense Mutations. - Zhe Zhang; Maria A. Miteva; Lin Wang; Emil Alexov (Comput. Math. Methods Medicine, 2012)

Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. - Chuan Li 003; Lin Li 003; Jie Zhang 035; Emil Alexov (J. Comput. Chem., 2012)

BION web server: predicting non-specifically bound surface ions. - Marharyta Petukh; Taylor Kimmet; Emil Alexov (Bioinform., 2013)

Research and applications: A rational free energy-based approach to understanding and targeting disease-causing missense mutations. - Zhe Zhang; Shawn Witham; Marharita Petukh; Gautier Moroy; Maria A. Miteva; Yoshihiko Ikeguchi; Emil Alexov (J. Am. Medical Informatics Assoc., 2013)

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi. - Chuan Li 003; Marharyta Petukh; Lin Li 003; Emil Alexov (J. Comput. Chem., 2013)

Enhancing Human Spermine Synthase Activity by Engineered Mutations. - Zhe Zhang; Yueli Zheng; Margo Petukh; Anthony Pegg; Yoshihiko Ikeguchi; Emil Alexov (PLoS Comput. Biol., 2013)

Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. - Praveen Nedumpully-Govindan; Lin Li 003; Emil Alexov; Mark A. Blenner; Feng Ding 002 (Bioinform., 2014)

ProBLM Web Server: Protein and Membrane Placement and Orientation Package. - Taylor Kimmet; Nicholas Smith; Shawn Witham; Marharyta Petukh; Subhra Sarkar; Emil Alexov (Comput. Math. Methods Medicine, 2014)

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi. - Roberta P. Dias; Lin Li 003; Thereza A. Soares; Emil Alexov (J. Comput. Chem., 2014)

Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. - Tugba G. Kucukkal; Emil Alexov (Comput. Math. Methods Medicine, 2015)

Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence. - Marharyta Petukh; Min Zhang; Emil Alexov (J. Comput. Chem., 2015)

Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. - Marharyta Petukh; Minghui Li; Emil Alexov (PLoS Comput. Biol., 2015)

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs. - Lin Wang; Min Zhang; Emil Alexov (Bioinform., 2016)

Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. - Arghya Chakravorty; Lin Li 003; Emil Alexov (J. Comput. Chem., 2016)

DelPhiForce web server: electrostatic forces and energy calculations and visualization. - Lin Li 003; Zhe Jia; Yunhui Peng; Arghya Chakravorty; Lexuan Sun; Emil Alexov (Bioinform., 2017)

Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. - Zhe Jia; Lin Li 003; Arghya Chakravorty; Emil Alexov (J. Comput. Chem., 2017)

DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. - Lin Li 003; Arghya Chakravorty; Emil Alexov (J. Comput. Chem., 2017)

Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. - Yunhui Peng; Lexuan Sun; Zhe Jia; Lin Li 003; Emil Alexov (Bioinform., 2018)

PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. - Swagata Pahari; Lexuan Sun; Emil Alexov (Database J. Biol. Databases Curation, 2019)

Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes. - Shailesh Kumar Panday; Mihiri H. B. Shashikala; Arghya Chakravorty; Shan Zhao 001; Emil Alexov (Commun. Inf. Syst., 2019)

A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. - Arghya Chakravorty; Emilio Gallicchio; Emil Alexov (J. Comput. Chem., 2019)

DelPhi Suite: New Developments and Review of Functionalities. - Chuan Li 003; Zhe Jia; Arghya Chakravorty; Swagata Pahari; Yunhui Peng; Sankar Basu; Mahesh Koirala; Shailesh Kumar Panday; Marharyta Petukh; Lin Li 003; Emil Alexov (J. Comput. Chem., 2019)

A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces. - Siwen Wang; Arum Lee; Emil Alexov; Shan Zhao 001 (Appl. Math. Lett., 2020)

Effects of Single-Nucleotide Polymorphisms in Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2): A Comprehensive Study. - Zoya Khalid; Omar Almaghrabi; Emil Alexov (Comput. Math. Methods Medicine, 2020)

Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. - Arghya Chakravorty; Shailesh Kumar Panday; Swagata Pahari; Shan Zhao 001; Emil Alexov (J. Chem. Inf. Model., 2020)

SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. - Gen Li; Swagata Pahari; Adithya Krishna Murthy; Siqi Liang 002; Robert Fragoza; Haiyuan Yu; Emil Alexov (Bioinform., 2021)

SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. - Gen Li; Shailesh Kumar Panday; Yunhui Peng; Emil Alexov (Bioinform., 2021)

A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions. - Siwen Wang; Yuanzhen Shao; Emil Alexov; Shan Zhao 001 (J. Comput. Phys., 2022)

Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: A unified regularization formulation. - Yuanzhen Shao; Mark McGowan; Siwen Wang; Emil Alexov; Shan Zhao 001 (Appl. Math. Comput., 2023)

Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential. - Shan Zhao 001; Idowu E. Ijaodoro; Mark McGowan; Emil Alexov (J. Comput. Phys., 2024)

On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model. - Shailesh Kumar Panday; Arghya Chakravorty; Shan Zhao 001; Emil Alexov (J. Comput. Chem., 2025)

In Silico Screening for Small Molecules to Alter Calpain Proteolysis through Modulating Conformation Changes Induced by Heterodimerization. - Pitambar Poudel; Ivan Shapovalov; Shailesh Kumar Panday; Kazem Nouri; Peter L. Davies; Peter A. Greer; Emil Alexov (J. Chem. Inf. Model., 2025)