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CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Journal of computational chemistry, 2013-09, Vol.34 (25), p.2135-2145

2013

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Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

Chemical reviews, 2019-07, Vol.119 (13), p.7940-7995

2019

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Nature methods, 2017-01, Vol.14 (1), p.71

2017

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Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

Journal of computational chemistry, 2012-12, Vol.33 (31), p.2451-2468

2012

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An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

Chemical reviews, 2016-05, Vol.116 (9), p.4983-5013

2016

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All-atom polarizable force field for DNA based on the classical drude oscillator model

Journal of computational chemistry, 2014-06, Vol.35 (16), p.1219-1239

2014

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Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide

Biophysical journal, 2014-08, Vol.107 (4), p.991-997

2014

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Computational fragment-based binding site identification by ligand competitive saturation

PLoS computational biology, 2009-07, Vol.5 (7), p.e1000435

2009

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FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

Journal of computational chemistry, 2020-04, Vol.41 (9), p.958-970

2020

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Force field development and simulations of intrinsically disordered proteins

Current opinion in structural biology, 2018-02, Vol.48, p.40-48

2018

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Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma

The Journal of clinical investigation, 2016-09, Vol.126 (9), p.3351-3362

2016

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Empirical force fields for biological macromolecules: Overview and issues

Journal of computational chemistry, 2004-10, Vol.25 (13), p.1584-1604

Mackerell Jr, Alexander D.

2004

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Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

Journal of chemical theory and computation, 2021-03, Vol.17 (3), p.1726-1741

2021

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Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

Journal of computational chemistry, 2011-07, Vol.32 (9), p.1929-1943

2011

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Polarizable force field for RNA based on the classical drude oscillator

Journal of computational chemistry, 2018-12, Vol.39 (32), p.2624-2646

2018

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Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field

Journal of chemical theory and computation, 2020-05, Vol.16 (5), p.3221-3239

2020

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CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

Biophysical journal, 2014-07, Vol.107 (1), p.134-145

2014

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Journal of chemical theory and computation, 2016-01, Vol.12 (1), p.405-413

2016

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Force Fields for Small Molecules

Methods in molecular biology (Clifton, N.J.), 2019, Vol.2022, p.21

2019

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Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

Bioorganic & medicinal chemistry, 2016-10, Vol.24 (20), p.4812-4825

2016

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Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

The journal of physical chemistry. B, 2010-06, Vol.114 (23), p.7830-7843

2010

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CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Journal of computational chemistry, 2022-02, Vol.43 (5), p.359-375

2022

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Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation

Biophysical journal, 2012-09, Vol.103 (5), p.1045-1051

2012

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Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?

The journal of physical chemistry. B, 2017-07, Vol.121 (28), p.6813-6821

2017

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CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

All-atom polarizable force field for DNA based on the classical drude oscillator model

Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide

Computational fragment-based binding site identification by ligand competitive saturation

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

Force field development and simulations of intrinsically disordered proteins

Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma

Empirical force fields for biological macromolecules: Overview and issues

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

Polarizable force field for RNA based on the classical drude oscillator

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Decoding the Signaling of a GPCR Heteromeric Complex Reveals a Unifying Mechanism of Action of Antipsychotic Drugs

Force Fields for Small Molecules

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation

Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?

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