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ORCIDEmil Alexov
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2020 – today
- 2024
[j37]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: 112634 (2024)- 2023
- [j36]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: 127501 (2023) - 2022
- [j35]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: 111340 (2022) - 2021
- [j34]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): 992-999 (2021) - [j33]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): 3760-3765 (2021) - 2020
- [j32]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: 106144 (2020) - [j31]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: 7419512:1-7419512:9 (2020) - [j30]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): 2229-2246 (2020)
2010 – 2019
- 2019
- [j29]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: baz024 (2019) - [j28]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): 405-423 (2019) - [j27]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): 1290-1304 (2019) - [j26]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): 2502-2508 (2019) - [i1]Siwen Wang, Arum Lee, Emil Alexov, Shan Zhao:
A regularization approach for solving Poisson's equation with singular charge sources and diffuse interfaces. CoRR abs/1910.00425 (2019) - 2018
- [j25]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): 779-786 (2018) - 2017
- [j24]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): 3661-3663 (2017) - [j23]Lin Li, Arghya Chakravorty, Emil Alexov:
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J. Comput. Chem. 38(9): 584-593 (2017) - [j22]Zhe Jia, Lin Li, Arghya Chakravorty, Emil Alexov:
Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J. Comput. Chem. 38(22): 1974-1979 (2017) - 2016
- [j21]Lin Wang, Min Zhang, Emil Alexov:
DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs. Bioinform. 32(4): 614-615 (2016) - [j20]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): 2495-2507 (2016) - 2015
- [j19]Tugba G. Kucukkal, Emil Alexov:
Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2. Comput. Math. Methods Medicine 2015: 746157:1-746157:9 (2015) - [j18]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): 2381-2393 (2015) - [j17]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) - 2014
- [j16]Praveen Nedumpully-Govindan, Lin Li, Emil Alexov, Mark A. Blenner, Feng Ding:
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinform. 30(16): 2302-2309 (2014) - [j15]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: 838259:1-838259:7 (2014) - [j14]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): 1418-1429 (2014) - 2013
- [j13]Marharyta Petukh, Taylor Kimmet, Emil Alexov:
BION web server: predicting non-specifically bound surface ions. Bioinform. 29(6): 805-806 (2013) - [j12]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): 643-651 (2013) - [j11]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): 1949-1960 (2013) - [j10]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) - 2012
- [j9]Zhe Zhang, Lin Wang, Yang Gao, Jie Zhang, Maxim Zhenirovskyy, Emil Alexov:
Predicting folding free energy changes upon single point mutations. Bioinform. 28(5): 664-671 (2012) - [j8]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): 1655-1657 (2012) - [j7]Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov:
Analyzing Effects of Naturally Occurring Missense Mutations. Comput. Math. Methods Medicine 2012: 805827:1-805827:15 (2012) - [j6]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): 1960-1966 (2012) - 2010
- [j5]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): 334-349 (2010)
2000 – 2009
- 2007
- [j4]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): 693-715 (2007) - [j3]Petras J. Kundrotas, Emil Alexov:
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. 35(Database-Issue): 575-579 (2007) - 2006
- [j2]Petras J. Kundrotas, Emil Alexov:
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinform. 7: 503 (2006) - 2002
- [j1]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): 128-137 (2002)
Coauthor Index
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