Computational Biophysics and Bioinformatics

Professor Emil Alexov Group


Journal Articles by Z. Jia

S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, et al.
Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]
Living Journal of Computational Molecular Science, 1(2), 10841, 2019
RIS, BibTex
Y. Peng, Y. Yang, L. Li, Z. Jia, W. Cao, and E. Alexov
DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme
Frontiers in molecular biosciences, 6, 74, 2019
RIS, BibTex
C. Li, Z. Jia, A. Chakravorty, S. Pahari, Y. Peng, S. Basu, M. Koirala, S. K. Panday, et al.
DelPhi suite: New developments and review of functionalities
Journal of computational chemistry, 40(28), 2502-2508, 2019
RIS, BibTex
A. Chakravorty, Z. Jia, Y. Peng, N. Tajielyato, L. Wang, and E. Alexov
Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents
Frontiers in molecular biosciences, 5, 25, 2018
RIS, BibTex
Z. Jia, L. Li, Y. Peng, F. Ding, and E. Alexov
The capricious electrostatic force: Revealing the signaling pathway in integrin α 2-I domain
Journal of Theoretical and Computational Chemistry, 17(3), 1840001, 2018
RIS, BibTex
A. Chakravorty, Z. Jia, L. Li, S. Zhao, and E. Alexov
Reproducing the ensemble average polar solvation energy of a protein from a single structure: gaussian-based smooth dielectric function for macromolecular modeling
Journal of chemical theory and computation, 14(2), 1020-1032, 2018
RIS, BibTex
Y. Peng, L. Sun, Z. Jia, L. Li, and E. Alexov
Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver
Bioinformatics, 34(5), 779-786, 2018
RIS, BibTex
L. Li, Z. Jia, Y. Peng, S. Godar, I. Getov, S. Teng, J. Alper, and E. Alexov
Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations
Scientific reports, 7(1), 1-12, 2017
RIS, BibTex
L. Li, Z. Jia, Y. Peng, A. Chakravorty, L. Sun, and E. Alexov
DelPhiForce web server: electrostatic forces and energy calculations and visualization
Bioinformatics, 33(22), 3661-3663, 2017
RIS, BibTex
A. Chakravorty, Z. Jia, L. Li, and E. Alexov
A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential
Langmuir, 33(9), 2283-2295, 2017
RIS, BibTex

Conference Papers

Z. Jia and E. Alexov
Simulation study of integrin alpha-2 I domain activation
RIS, BibTex


Z. Jia, L. Li, A. Chakravorty, and E. Alexov
Treating ion distribution with G aussian-based smooth dielectric function in DelPhi
RIS, BibTex
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