Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. (Q42199119)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

title

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

0 references

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

Alex MacKerell

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

author name string

A D MacKerell

series ordinal

2

1 reference

18 October 2017

28 November 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Information and Modeling

17 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

volume

52

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

issue

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

page(s)

3144-3154

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

17 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=3528824

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Structure and dynamics of the M3 muscarinic acetylcholine receptor

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

How fast-folding proteins fold

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Open Babel: An open chemical toolbox

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Molecular basis of ligand dissociation in β-adrenergic receptors

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

The free energy landscape of small molecule unbinding

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Structure and function of an irreversible agonist-β(2) adrenoceptor complex

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Finding Chemical Records by Digital Computers

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Automatic atom type and bond type perception in molecular mechanical calculations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Empirical force fields for biological macromolecules: overview and issues.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

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

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Development and testing of a general amber force field

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Counterexamples in chemical ring perception.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Improved treatment of the protein backbone in empirical force fields.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528824

Computer program for finding all possible cycles in graphs

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23146088

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CI300363C

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

journals/jcisd/VanommeslaegheM12

17 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23146088%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

PubMed publication ID

23146088

1 reference