| 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 | 1660 | 2012 |
| 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 | 678 | 2011 |
| 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 | 214 | 2010 |
| 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 | 143 | 2011 |
| 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 | 140 | 2013 |
| 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 | 93 | 2015 |
| 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 | 87 | 2011 |
| 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 | 83 | 2014 |
| 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 | 79 | 2014 |
| 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 | 67 | 2015 |
| 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 | 64 | 2020 |
| Molecular dynamics simulations of ibuprofen binding to Aβ peptides EP Raman, T Takeda, DK Klimov Biophysical journal 97 (7), 2070-2079, 2009 | 63 | 2009 |
| 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 | 53 | 2015 |
| 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 | 45 | 2015 |
| 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 | 40 | 2012 |
| 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 | 39 | 2011 |
| 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 | 39 | 2010 |
| Molecular dynamics simulations of anti-aggregation effect of ibuprofen WE Chang, T Takeda, EP Raman, DK Klimov Biophysical journal 98 (11), 2662-2670, 2010 | 38 | 2010 |
| 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 | 33 | 2017 |
| Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B LE McKnight, EP Raman, P Bezawada, S Kudrimoti, PT Wilder, ... ACS medicinal chemistry letters 3 (12), 975-979, 2012 | 29 | 2012 |
Kenno VanommeslaegheVrije Universiteit BrusselVerified email at kenno.org