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

Journal of chemical information and modeling, 2012-12, Vol.52 (12), p.3155-3168

2012

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

Journal of chemical information and modeling, 2013-12, Vol.53 (12), p.3384-3398

2013

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CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

Journal of chemical theory and computation, 2011-10, Vol.7 (10), p.3162-3180

2011

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CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses

The journal of physical chemistry. B, 2010-10, Vol.114 (40), p.12981-12994

2010

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

Journal of chemical information and modeling, 2011-04, Vol.51 (4), p.877-896

2011

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

Journal of chemical information and modeling, 2015-03, Vol.55 (3), p.700-708

2015

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Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein–Ligand Binding: Binding Site Variability

Journal of the American Chemical Society, 2015-02, Vol.137 (7), p.2608-2621

2015

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Rapid estimation of hydration thermodynamics of macromolecular regions

The Journal of chemical physics, 2013-08, Vol.139 (5), p.055105-055105

2013

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

Biochemical journal, 2015-05, Vol.467 (3), p.425-438

2015

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

Journal of chemical information and modeling, 2019-06, Vol.59 (6), p.2690-2701

Raman, E. Prabhu

2019

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

Journal of chemical theory and computation, 2020-12, Vol.16 (12), p.7895-7914

2020

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

Journal of chemical information and modeling, 2011-01, Vol.51 (1), p.148-158

2011

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

Journal of chemical information and modeling, 2015-02, Vol.55 (2), p.407-420

2015

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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, 2014-06, Vol.10 (6), p.2281-2290

2014

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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, 2017-06, Vol.38 (15), p.1238-1251

2017

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

Journal of computer-aided molecular design, 2014-05, Vol.28 (5), p.491-507

2014

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

Methods in molecular biology (Clifton, N.J.), 2015, Vol.1289, p.75

2015

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Nonsteroidal Anti-inflammatory Drug Naproxen Destabilizes Aβ Amyloid Fibrils: A Molecular Dynamics Investigation

The journal of physical chemistry. B, 2010-11, Vol.114 (46), p.15394-15402

2010

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

Journal of chemical theory and computation, 2012-10, Vol.8 (10), p.3513-3525

2012

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Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters

The journal of physical chemistry. B, 2011-01, Vol.115 (3), p.487-499

2011

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

Journal of medicinal chemistry, 2016-01, Vol.59 (2), p.592-608

2016

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Molecular Dynamics Simulations of Anti-Aggregation Effect of Ibuprofen

Biophysical journal, 2010-06, Vol.98 (11), p.2662-2670

2010

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

Acta crystallographica. Section D, Structural biology, 2016-06, Vol.72 (Pt 6), p.753

2016

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

ACS medicinal chemistry letters, 2012-12, Vol.3 (12), p.975-979

2012

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Folding of tandem-linked domains

Proteins, structure, function, and bioinformatics, 2007-06, Vol.67 (4), p.795-810

2007

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

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

CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses

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

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

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein–Ligand Binding: Binding Site Variability

Rapid estimation of hydration thermodynamics of macromolecular regions

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

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

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

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

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

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

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

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

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

Nonsteroidal Anti-inflammatory Drug Naproxen Destabilizes Aβ Amyloid Fibrils: A Molecular Dynamics Investigation

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

Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force Field Parameters

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

Molecular Dynamics Simulations of Anti-Aggregation Effect of Ibuprofen

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

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

Folding of tandem-linked domains

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