Emil Alexov

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 19

Top Topics

Predicting Protein

Top Venues

J. Comput. Chem.

Comput. Math. Methods Medicine

J. Comput. Phys.

Publications

Shan Zhao, Idowu E. Ijaodoro, Mark McGowan, Emil Alexov
Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential. J. Comput. Phys. 497 (2024)
Yuanzhen Shao, Mark McGowan, Siwen Wang, Emil Alexov, Shan Zhao
Convergence of a diffuse interface Poisson-Boltzmann (PB) model to the sharp interface PB model: A unified regularization formulation. Appl. Math. Comput. 436 (2023)
Siwen Wang, Yuanzhen Shao, Emil Alexov, Shan Zhao
A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions. J. Comput. Phys. 464 (2022)
Gen Li, Shailesh Kumar Panday, Yunhui Peng, Emil Alexov
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. Bioinform. 37 (21) (2021)
Gen Li, Swagata Pahari, Adithya Krishna Murthy, Siqi Liang, Robert Fragoza, Haiyuan Yu, Emil Alexov
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. Bioinform. 37 (7) (2021)
Arghya Chakravorty, Shailesh Kumar Panday, Swagata Pahari, Shan Zhao, Emil Alexov
Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. J. Chem. Inf. Model. 60 (4) (2020)
Siwen Wang, Arum Lee, Emil Alexov, Shan Zhao
A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces. Appl. Math. Lett. 102 (2020)
Zoya Khalid, Omar Almaghrabi, Emil Alexov
Effects of Single-Nucleotide Polymorphisms in Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2): A Comprehensive Study. Comput. Math. Methods Medicine 2020 (2020)
Siwen Wang, Arum Lee, Emil Alexov, Shan Zhao
A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces. CoRR (2019)
Swagata Pahari, Lexuan Sun, Emil Alexov
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database J. Biol. Databases Curation 2019 (2019)
Chuan Li, Zhe Jia, Arghya Chakravorty, Swagata Pahari, Yunhui Peng, Sankar Basu, Mahesh Koirala, Shailesh Kumar Panday, Marharyta Petukh, Lin Li, Emil Alexov
DelPhi Suite: New Developments and Review of Functionalities. J. Comput. Chem. 40 (28) (2019)
Shailesh Kumar Panday, Mihiri H. B. Shashikala, Arghya Chakravorty, Shan Zhao, Emil Alexov
Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes. Commun. Inf. Syst. 19 (4) (2019)
Arghya Chakravorty, Emilio Gallicchio, Emil Alexov
A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. J. Comput. Chem. 40 (12) (2019)
Yunhui Peng, Lexuan Sun, Zhe Jia, Lin Li, Emil Alexov
Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. Bioinform. 34 (5) (2018)
Lin Li, Arghya Chakravorty, Emil Alexov
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J. Comput. Chem. 38 (9) (2017)
Zhe Jia, Lin Li, Arghya Chakravorty, Emil Alexov
Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J. Comput. Chem. 38 (22) (2017)
Lin Li, Zhe Jia, Yunhui Peng, Arghya Chakravorty, Lexuan Sun, Emil Alexov
DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinform. 33 (22) (2017)
Arghya Chakravorty, Lin Li, Emil Alexov
Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols. J. Comput. Chem. 37 (28) (2016)
Lin Wang, Min Zhang, Emil Alexov
of proteins, RNAs and DNAs. Bioinform. 32 (4) (2016)
Marharyta Petukh, Minghui Li, Emil Alexov
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PLoS Comput. Biol. 11 (7) (2015)
Tugba G. Kucukkal, Emil Alexov
Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. Comput. Math. Methods Medicine 2015 (2015)
Marharyta Petukh, Min Zhang, Emil Alexov
Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence. J. Comput. Chem. 36 (32) (2015)
Praveen Nedumpully-Govindan, Lin Li, Emil Alexov, Mark A. Blenner, Feng Ding
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinform. 30 (16) (2014)
Taylor Kimmet, Nicholas Smith, Shawn Witham, Marharyta Petukh, Subhra Sarkar, Emil Alexov
ProBLM Web Server: Protein and Membrane Placement and Orientation Package. Comput. Math. Methods Medicine 2014 (2014)
Roberta P. Dias, Lin Li, Thereza A. Soares, Emil Alexov
Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi. J. Comput. Chem. 35 (19) (2014)
Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov
Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi. J. Comput. Chem. 34 (22) (2013)
Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov
Enhancing Human Spermine Synthase Activity by Engineered Mutations. PLoS Comput. Biol. 9 (2) (2013)
Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria A. Miteva, Yoshihiko Ikeguchi, Emil Alexov
Research and applications: A rational free energy-based approach to understanding and targeting disease-causing missense mutations. J. Am. Medical Informatics Assoc. 20 (4) (2013)
Marharyta Petukh, Taylor Kimmet, Emil Alexov
BION web server: predicting non-specifically bound surface ions. Bioinform. 29 (6) (2013)
Chuan Li, Lin Li, Jie Zhang, Emil Alexov
Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. J. Comput. Chem. 33 (24) (2012)
Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov
Analyzing Effects of Naturally Occurring Missense Mutations. Comput. Math. Methods Medicine 2012 (2012)
Nicholas Smith, Shawn Witham, Subhra Sarkar, Jie Zhang, Lin Li, Chuan Li, Emil Alexov
DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. Bioinform. 28 (12) (2012)
Zhe Zhang, Lin Wang, Yang Gao, Jie Zhang, Maxim Zhenirovskyy, Emil Alexov
Predicting folding free energy changes upon single point mutations. Bioinform. 28 (5) (2012)
Shaolei Teng, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov, Liangjiang Wang
Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein-protein interaction. Int. J. Comput. Biol. Drug Des. 3 (4) (2010)
Petras J. Kundrotas, Paulina Georgieva, Alexandra Shosheva, Petya Christova, Emil Alexov
Assessing the Quality of the Homology-Modeled 3D Structures from electrostatic Standpoint: Test on bacterial nucleoside monophosphate kinase Families. J. Bioinform. Comput. Biol. 5 (3) (2007)
Petras J. Kundrotas, Emil Alexov
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. 35 (Database-Issue) (2007)
Petras J. Kundrotas, Emil Alexov
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinform. 7 (2006)
Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig
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. 23 (1) (2002)