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E. Prabhu Raman
E. Prabhu Raman
Nurix Therapeutics
Verified email at nurixtx.com - Homepage
Title
Cited by
Cited by
Year
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
K Vanommeslaeghe, EP Raman, AD MacKerell Jr
Journal of chemical information and modeling 52 (12), 3155-3168, 2012
15092012
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling
O Guvench, SS Mallajosyula, EP Raman, E Hatcher, K Vanommeslaeghe, ...
Journal of Chemical Theory and Computation 7 (10), 3162-3180, 2011
6222011
CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses
EP Raman, O Guvench, AD MacKerell Jr
The Journal of Physical Chemistry B 114 (40), 12981-12994, 2010
2022010
Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations
EP Raman, W Yu, O Guvench, AD MacKerell Jr
Journal of chemical information and modeling 51 (4), 877-896, 2011
1342011
Inclusion of multiple fragment types in the Site Identification by Ligand Competitive Saturation (SILCS) approach
EP Raman, W Yu, SK Lakkaraju, AD MacKerell Jr
Journal of chemical information and modeling 53 (12), 3384-3398, 2013
1282013
Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters
S Abel, FY Dupradeau, EP Raman, AD MacKerell Jr, M Marchi
The Journal of Physical Chemistry B 115 (3), 487-499, 2011
872011
Pharmacophore modeling using Site-Identification by Ligand Competitive Saturation (SILCS) with multiple probe molecules
W Yu, SK Lakkaraju, EP Raman, L Fang, AD MacKerell Jr
Journal of chemical information and modeling 55 (2), 407-420, 2015
832015
Sampling of Organic Solutes in Aqueous and Heterogeneous Environments using Oscillating Excess Chemical Potentials in Grand Canonical-Like Monte Carlo-Molecular Dynamics …
SK Lakkaraju, EP Raman, W Yu, AD MacKerell
Journal of Chemical Theory and Computation, 2014
742014
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
W Yu, SK Lakkaraju, EP Raman, AD MacKerell Jr
Journal of computer-aided molecular design 28 (5), 491-507, 2014
732014
Molecular dynamics simulations of ibuprofen binding to Aβ peptides
EP Raman, T Takeda, DK Klimov
Biophysical journal 97 (7), 2070-2079, 2009
622009
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors
SK Lakkaraju, W Yu, EP Raman, AV Hershfeld, L Fang, DA Deshpande, ...
Journal of chemical information and modeling 55 (3), 700-708, 2015
592015
Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics
EP Raman, TJ Paul, RL Hayes, CL Brooks III
Journal of Chemical Theory and Computation 16 (12), 7895-7914, 2020
512020
Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design
CE Faller, EP Raman, AD MacKerell, O Guvench
Fragment-Based Methods in Drug Discovery, 75-87, 2015
462015
Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf
R Samadani, J Zhang, A Brophy, T Oashi, UD Priyakumar, EP Raman, ...
The Biochemical Journal 467 (3), 425, 2015
412015
Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations
EP Raman, K Vanommeslaeghe, AD MacKerell Jr
Journal of Chemical Theory and Computation, 2012
402012
Binding of nonsteroidal anti‐inflammatory drugs to Aβ fibril
T Takeda, WE Chang, EP Raman, DK Klimov
Proteins: Structure, Function, and Bioinformatics 78 (13), 2849-2860, 2010
372010
Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness
T Oashi, AL Ringer, EP Raman, AD MacKerell Jr
Journal of chemical information and modeling 51 (1), 148-158, 2011
332011
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 …
EP Raman, SK Lakkaraju, RA Denny, AD MacKerell
Journal of computational chemistry 38 (15), 1238-1251, 2017
322017
Molecular dynamics simulations of anti-aggregation effect of ibuprofen
WE Chang, T Takeda, EP Raman, DK Klimov
Biophysical journal 98 (11), 2662-2670, 2010
322010
Nonsteroidal anti-inflammatory drug naproxen destabilizes Aβ amyloid fibrils: a molecular dynamics investigation
T Takeda, R Kumar, EP Raman, DK Klimov
The Journal of Physical Chemistry B 114 (46), 15394-15402, 2010
292010
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