E. Prabhu Raman

Dassault Systèmes (United States) — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

23h-index3.8kcitations35works0.02yr avg
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Research Topics

Protein Structure and Dynamics(26), Computational Drug Discovery Methods(20), Enzyme Structure and Function(7), Monoclonal and Polyclonal Antibodies Research(4), RNA and protein synthesis mechanisms(3)

Publications35 total

Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics
Journal of Chemical Theory and Computation·2020· 73 citedOpen Access
Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free Energy Calculations using Lambda Dynamics
2020Open Access
Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free Energy Calculations using Lambda Dynamics
2020· 5 citedOpen Access
Template-Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands
Journal of Chemical Information and Modeling·2019· 4 cited
Estimation of relative free energies of binding using pre‐computed ensembles based on the single‐step free energy perturbation and the site‐identification by Ligand competitive saturation approaches
Journal of Computational Chemistry·2016· 34 citedOpen Access
Novel protein–inhibitor interactions in site 3 of Ca<sup>2+</sup>-bound S100B as discovered by X-ray crystallography
Acta Crystallographica Section D Structural Biology·2016· 11 citedOpen Access
Small Molecule Inhibitors of Ca<sup>2+</sup>-S100B Reveal Two Protein Conformations
Journal of Medicinal Chemistry·2016· 15 citedOpen Access
Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf
Biochemical Journal·2015· 41 cited
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors
Journal of Chemical Information and Modeling·2015· 62 citedOpen Access
Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein–Ligand Binding: Binding Site Variability
Journal of the American Chemical Society·2015· 27 citedOpen Access
Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules
Journal of Chemical Information and Modeling·2015· 80 cited
Pharmacophore Modeling using Site-Identification by Ligand Competitive Saturation (SILCS) Method with Multiple Probe Molecules
Biophysical Journal·2015· 52 citedOpen Access
Molecular Understanding of the Binding of Macrolide Antibiotics to the Ribosome using Site-Identification via Ligand Competitive Saturation
Biophysical Journal·2015Open Access
Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design
Methods in molecular biology·2015· 54 citedOpen Access
Quantifying the Thermodynamic Molecular Driving Forces in Protein-Ligand Binding
Biophysical Journal·2015Open Access
Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations
Journal of Chemical Theory and Computation·2014· 97 cited
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
Journal of Computer-Aided Molecular Design·2014· 67 citedOpen Access
Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach
Journal of Chemical Information and Modeling·2013· 130 citedOpen Access
Rapid estimation of hydration thermodynamics of macromolecular regions
The Journal of Chemical Physics·2013· 24 citedOpen Access
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
Journal of Chemical Information and Modeling·2012· 1.7k cited
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Frequent Co-authors

Alexander D. MacKerell(23), Wenbo Yu(9), Sirish Kaushik Lakkaraju(8), Dmitri K. Klimov(7), Takako Takeda(6), Olgun Guvench(4), Lei Fang(4), Kenno Vanommeslaeghe(3), Thomas J. Paul(3), Ryan L. Hayes(3), Charles L. Brooks(3), Wenling E. Chang(3), Paul T. Wilder(3), David J. Weber(3), Taiji Oashi(2), Laura E. McKnight(2), Padmavani Bezawada(2), Eric A. Toth(2), Andrew Coop(2), Michael C. Cavalier(2)