Publications in VIVO

Co-author Network

Jagdish Suresh Patel Research Assistant Professor

Positions

Research Assistant Professor, Biological Sciences , College of Science 2015 -

Dr. Patel uses molecular dynamics and enhanced sampling techniques for studying "rare events" such as protein-ligand interactions, protein-protein interactions, folding/unfolding, and ion transfer via protein channels. He has experience in protein structure prediction using homology modeling, sequence analysis, modeling drug-target interactions using docking, virtual screening of libraries of small molecules against its target to identify 'hits' and prediction of their physio-chemical properties. He also performs free energy calculations to test the effects of mutations on molecular structure and is developing new approaches for calculating free energy with speed & accuracy and molecular dynamics simulations of systems involving protein, DNA and RNA molecular models.

Publications

selected publications

academic article
- Implementing and Assessing an Alchemical Method for Calculating Protein-Protein Binding Free Energy. Journal of Chemical Theory and Computation. 17:2457-2464. 2021
- Assessment of Software Methods for Estimating Protein-protein Relative Binding Affinities. PLOS One. 15:e0240573. 2020
- Short-wavelength-sensitive 2 (Sws2) Visual Photopigment Models Combined with Atomistic Molecular Simulations to Predict Spectral Peaks of Absorbance. PLOS Computational Biology. 16:e1008212. 2020
- Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness. PLOS One. 15:e0233509. 2020
- Electrostatic Switching Controls Channel Dynamics of the Sensor Protein VirB10 in A. tumefaciens Type IV Secretion System. ACS Omega. 5:3271-3281. 2020
- Calculation of Protein-Protein Binding Free Energies using Umbrella Sampling with Dual Resolution Water Models. Biophysical Journal. 116:291A-291A. 2019
- Vision using multiple distinct rod opsins in deep-sea fishes. Science (New York, N.Y). 364:588. 2019
- Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations. Investigative Ophthalmology and Visual Science. 14:blank. 2018
- Fast Calculation of Protein–Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model. Journal of Chemical Theory and Computation. 14:991-997. 2018
- Predicting Spectral Shift in the Teleost Rh2 Cone Opsins using Molecular Dynamics Simulations. Biophysical Journal. 114:338A-338A. 2018
- Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression.. Molecular Biology and Evolution. 34:2839-2855. 2017

Contact

full name

Jagdish Suresh Patel