E. P. Raman

发表

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

Alexander D. MacKerell, Kenno Vanommeslaeghe, Olgun Guvench, 2011, Journal of chemical theory and computation.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2010, The journal of physical chemistry. B.

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations

Alexander D. MacKerell, E. Prabhu Raman, Sirish Kaushik Lakkaraju, 2014, Journal of chemical theory and computation.

Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design.

Alexander D. MacKerell, Olgun Guvench, E. P. Raman, 2015, Methods in molecular biology.

Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics.

Thomas J. Paul, C. Brooks, R. L. Hayes, 2020, Journal of chemical theory and computation.

Molecular Dynamics Simulations of Ibuprofen Binding to Ab Peptides

D. Klimov, E. P. Raman, Takako Takeda, 2009 .

Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf.

Alexander D. MacKerell, U. D. Priyakumar, S. Fletcher, 2015, The Biochemical journal.

Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters.

Alexander D. MacKerell, M. Marchi, E. P. Raman, 2011, The journal of physical chemistry. B.

Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations.

Alexander D. MacKerell, M. I. Ansari, David J Weber, 2016, Journal of medicinal chemistry.

Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B.

Alexander D. MacKerell, David J Weber, R. Godoy-Ruiz, 2012, ACS medicinal chemistry letters.

Binding of nonsteroidal anti‐inflammatory drugs to Aβ fibril

D. Klimov, E. P. Raman, Wenling E. Chang, 2010, Proteins.

Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness

Alexander D. MacKerell, Taiji Oashi, Ashley L. Ringer, 2011, J. Chem. Inf. Model..

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

Alexander D. MacKerell, E. Prabhu Raman, K. Vanommeslaeghe, 2012, J. Chem. Inf. Model..

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules

Alexander D. MacKerell, Lei Fang, Wenbo Yu, 2015, J. Chem. Inf. Model..

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2011, J. Chem. Inf. Model..

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2013, J. Chem. Inf. Model..

Rapid estimation of hydration thermodynamics of macromolecular regions.

Alexander D. MacKerell, Alexander D MacKerell, E Prabhu Raman, 2013, The Journal of chemical physics.

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors

Alexander D. MacKerell, Lei Fang, Wenbo Yu, 2015, J. Chem. Inf. Model..

Molecular dynamics simulations of anti-aggregation effect of ibuprofen.

D. Klimov, E. P. Raman, Wenling E. Chang, 2010, Biophysical journal.

Molecular dynamics simulations of Ibuprofen binding to Abeta peptides.

D. Klimov, E. P. Raman, Takako Takeda, 2009, Biophysical journal.

Mechanical Unbinding of Aβ Peptides from Amyloid Fibrils

D. Klimov, V. Barsegov, E. P. Raman, 2007 .

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

Alexander D. MacKerell, E. Prabhu Raman, Sirish Kaushik Lakkaraju, 2017, J. Comput. Chem..

Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography.

Alexander D. MacKerell, David J Weber, M. Cavalier, 2016, Acta crystallographica. Section D, Structural biology.

Pharmacophore Modeling using Site-Identification by Ligand Competitive Saturation (SILCS) Method with Multiple Probe Molecules

Lei Fang, Alexander D. MacKerell, E. Prabhu Raman, 2015 .

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2014, J. Comput. Aided Mol. Des..

Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations.

Alexander D. MacKerell, E. P. Raman, K. Vanommeslaeghe, 2012, Journal of Chemical Theory and Computation.

Template-Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands

E Prabhu Raman, E. P. Raman, 2019, J. Chem. Inf. Model..

Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability.

Alexander D. MacKerell, E. P. Raman, 2015, Journal of the American Chemical Society.

Molecular dynamics simulations of anti-aggregation effect of ibuprofen.

D. Klimov, E. P. Raman, Wenling E. Chang, 2010, Biophysical journal.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Alexander D. MacKerell, Olgun Guvench, E. P. Raman, 2010, The journal of physical chemistry. B.

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

Alexander D. MacKerell, E. P. Raman, K. Vanommeslaeghe, 2012, J. Chem. Inf. Model..

Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters.

Alexander D. MacKerell, M. Marchi, E. P. Raman, 2011, The journal of physical chemistry. B.

Folding of tandem‐linked domains

D. Klimov, V. Barsegov, E. P. Raman, 2007, Proteins.