(Q24632987)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19575467%20AND%20SRC:MED&resulttype=core&format=json

1 February 2020

title

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields (English)

1 reference

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1 February 2020

1 reference

1 reference

1

1 reference

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1 February 2020

Alex MacKerell

11

1 reference

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1 February 2020

author name string

E Hatcher

2

1 reference

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1 February 2020

C Acharya

3

1 reference

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1 February 2020

S Kundu

4

1 reference

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1 February 2020

S Zhong

5

1 reference

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1 February 2020

J Shim

6

1 reference

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1 February 2020

E Darian

7

1 reference

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1 February 2020

O Guvench

8

1 reference

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1 February 2020

P Lopes

9

1 reference

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1 February 2020

I Vorobyov

10

1 reference

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1 February 2020

language of work or name

English

0 references

publication date

1 March 2010

1 reference

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Journal of Computational Chemistry

1 February 2020

published in

1 reference

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1 February 2020

volume

31

1 reference

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1 February 2020

issue

4

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1 February 2020

page(s)

671-690

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CHARMM: the biomolecular simulation program

1 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

All-atom empirical potential for molecular modeling and dynamics studies of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Scalable molecular dynamics with NAMD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

The Amber biomolecular simulation programs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Development and testing of a general amber force field

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Automatic atom type and bond type perception in molecular mechanical calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Canonical dynamics: Equilibrium phase-space distributions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Additive empirical force field for hexopyranose monosaccharides

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Automated conformational energy fitting for force-field development.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

A computational study of nucleosomal DNA flexibility

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Ion selectivity in potassium channels

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Simulating movement of tRNA into the ribosome during decoding

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Empirical force fields for biological macromolecules: overview and issues.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Pseudorotation motion in tetrahydrofuran: an ab initio study

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Improved treatment of the protein backbone in empirical force fields.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Stereochemistry of nucleic acids and their constituents. XVIII. Conformational analysis of .alpha. nucleosides by x-ray crystallography

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888302

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

28 November 2018

1 reference

12 December 2020

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

1 reference

12 December 2020

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

7 January 2021

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

1 reference

7 January 2021

New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities

1 reference

7 January 2021

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

7 January 2021

Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets To Probe the Mechanism of Base Flipping byHhaI DNA (Cytosine C5)-methyltransferase

1 reference

7 January 2021

Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives

1 reference

7 January 2021

Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain−Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations

1 reference

7 January 2021

An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest

1 reference

7 January 2021

Comparison of simple potential functions for simulating liquid water

1 reference

7 January 2021

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

7 January 2021

A molecular dynamics method for simulations in the canonical ensemble

1 reference

7 January 2021

Identifiers

DOI

10.1002/JCC.21367

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19575467%20AND%20SRC:MED&resulttype=core&format=json

journals/jcc/VanommeslaegheHAKZSDGLVM10

1 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19575467%20AND%20SRC:MED&resulttype=core&format=json

1 February 2020

2 references