Emil Alexov - RankMe

42 papers Journal 42

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Accurate and Scalable Continuum Electrostatics for Large Biomolecular Systems: The J. Chem. Inf. Model. Shailesh Kumar Panday, Shan Zhao, Emil Alexov
2026	J	`jnl`	On generalizing the induced surface charge method to heterogeneous Poisson-Boltzmann models for electrostatic free energy calculation. J. Comput. Phys. Idowu E. Ijaodoro, Yuanzhen Shao, Emil Alexov, Shan Zhao
2025	J	`jnl`	On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model. J. Comput. Chem. Shailesh Kumar Panday, Arghya Chakravorty, Shan Zhao, Emil Alexov
2024	J	`jnl`	Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential. J. Comput. Phys. Shan Zhao, Idowu E. Ijaodoro, Mark McGowan, Emil Alexov
2024	J	`jnl`	SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein-protein complexes. Bioinform. Prawin Rimal, Shailesh Kumar Panday, Wang Xu, Yunhui Peng, Emil Alexov
2023	J	`jnl`	Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: A unified regularization formulation. Appl. Math. Comput. Yuanzhen Shao, Mark McGowan, Siwen Wang, Emil Alexov, Shan Zhao
2022	J	`jnl`	A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions. J. Comput. Phys. Siwen Wang, Yuanzhen Shao, Emil Alexov, Shan Zhao
2021	J	`jnl`	SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. Bioinform. Gen Li, Swagata Pahari, Adithya Krishna Murthy, Siqi Liang, Robert Fragoza, Haiyuan Yu, Emil Alexov
2021	J	`jnl`	SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. Bioinform. Gen Li, Shailesh Kumar Panday, Yunhui Peng, Emil Alexov
2020	J	`jnl`	A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces. Appl. Math. Lett. Siwen Wang, Arum Lee, Emil Alexov, Shan Zhao
2020	J	`jnl`	Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. J. Chem. Inf. Model. Arghya Chakravorty, Shailesh Kumar Panday, Swagata Pahari, Shan Zhao, Emil Alexov
2020	J	`jnl`	Effects of Single-Nucleotide Polymorphisms in Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2): A Comprehensive Study. Comput. Math. Methods Medicine Zoya Khalid, Omar Almaghrabi, Emil Alexov
2019	J	`jnl`	A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. J. Comput. Chem. Arghya Chakravorty, Emilio Gallicchio, Emil Alexov
2019	J	`jnl`	A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces. CoRR Siwen Wang, Arum Lee, Emil Alexov, Shan Zhao
2019	J	`jnl`	DelPhi Suite: New Developments and Review of Functionalities. J. Comput. Chem. Chuan Li, Zhe Jia, Arghya Chakravorty, Swagata Pahari, Yunhui Peng, Sankar Basu, Mahesh Koirala, Shailesh Kumar Panday, Marharyta Petukh, Lin Li, Emil Alexov
2019	J	`jnl`	PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database J. Biol. Databases Curation Swagata Pahari, Lexuan Sun, Emil Alexov
2019	J	`jnl`	Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes. Commun. Inf. Syst. Shailesh Kumar Panday, Mihiri H. B. Shashikala, Arghya Chakravorty, Shan Zhao, Emil Alexov
2018	J	`jnl`	Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. Bioinform. Yunhui Peng, Lexuan Sun, Zhe Jia, Lin Li, Emil Alexov
2017	J	`jnl`	DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinform. Lin Li, Zhe Jia, Yunhui Peng, Arghya Chakravorty, Lexuan Sun, Emil Alexov
2017	J	`jnl`	DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J. Comput. Chem. Lin Li, Arghya Chakravorty, Emil Alexov
2017	J	`jnl`	Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J. Comput. Chem. Zhe Jia, Lin Li, Arghya Chakravorty, Emil Alexov
2016	J	`jnl`	DelPhiPKa web server: predicting p Bioinform. Lin Wang, Min Zhang, Emil Alexov
2016	J	`jnl`	Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. J. Comput. Chem. Arghya Chakravorty, Lin Li, Emil Alexov
2015	J	`jnl`	Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PLoS Comput. Biol. Marharyta Petukh, Minghui Li, Emil Alexov
2015	J	`jnl`	Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence. J. Comput. Chem. Marharyta Petukh, Min Zhang, Emil Alexov
2015	J	`jnl`	Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. Comput. Math. Methods Medicine Tugba G. Kucukkal, Emil Alexov
2014	J	`jnl`	Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi. J. Comput. Chem. Roberta P. Dias, Lin Li, Thereza A. Soares, Emil Alexov
2014	J	`jnl`	ProBLM Web Server: Protein and Membrane Placement and Orientation Package. Comput. Math. Methods Medicine Taylor Kimmet, Nicholas Smith, Shawn Witham, Marharyta Petukh, Subhra Sarkar, Emil Alexov
2014	J	`jnl`	Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinform. Praveen Nedumpully-Govindan, Lin Li, Emil Alexov, Mark A. Blenner, Feng Ding
2013	J	`jnl`	BION web server: predicting non-specifically bound surface ions. Bioinform. Marharyta Petukh, Taylor Kimmet, Emil Alexov
2013	J	`jnl`	Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi. J. Comput. Chem. Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov
2013	J	`jnl`	Enhancing Human Spermine Synthase Activity by Engineered Mutations. PLoS Comput. Biol. Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov
2013	J	`jnl`	Research and applications: A rational free energy-based approach to understanding and targeting disease-causing missense mutations. J. Am. Medical Informatics Assoc. Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria A. Miteva, Yoshihiko Ikeguchi, Emil Alexov
2012	J	`jnl`	Analyzing Effects of Naturally Occurring Missense Mutations. Comput. Math. Methods Medicine Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov
2012	J	`jnl`	DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. Bioinform. Nicholas Smith, Shawn Witham, Subhra Sarkar, Jie Zhang, Lin Li, Chuan Li, Emil Alexov
2012	J	`jnl`	Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. J. Comput. Chem. Chuan Li, Lin Li, Jie Zhang, Emil Alexov
2012	J	`jnl`	Predicting folding free energy changes upon single point mutations. Bioinform. Zhe Zhang, Lin Wang, Yang Gao, Jie Zhang, Maxim Zhenirovskyy, Emil Alexov
2010	J	`jnl`	Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interaction. Int. J. Comput. Biol. Drug Des. Shaolei Teng, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov, Liangjiang Wang
2007	J	`jnl`	Assessing the Quality of the Homology-Modeled 3D Structures from electrostatic Standpoint: Test on bacterial nucleoside monophosphate kinase Families. J. Bioinform. Comput. Biol. Petras J. Kundrotas, Paulina Georgieva, Alexandra Shosheva, Petya Christova, Emil Alexov
2007	J	`jnl`	PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. Petras J. Kundrotas, Emil Alexov
2006	J	`jnl`	Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinform. Petras J. Kundrotas, Emil Alexov
2002	J	`jnl`	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. J. Comput. Chem. Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig