Rapid parameterization of small molecules using the Force Field Toolkit (Q37417543)

20 August 2017

Rapid parameterization of small molecules using the Force Field Toolkit (English)

1 reference

20 August 2017

0 references

4

1 reference

20 August 2017

3

Klaus Schulten

1 reference

20 August 2017

5

James C Gumbart

1 reference

20 August 2017

2

Jan Saam

1 reference

20 August 2017

Christopher G Mayne

1

1 reference

20 August 2017

2 September 2013

1 reference

Journal of Computational Chemistry

20 August 2017

1 reference

20 August 2017

34

1 reference

20 August 2017

32

1 reference

20 August 2017

2757-2770

1 reference

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

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

The future of molecular dynamics simulations in drug discovery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

MATCH: an atom-typing toolset for molecular mechanics force fields.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Molecular dynamics simulations and drug discovery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

SwissParam: A fast force field generation tool for small organic molecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Automated conformational energy fitting for force-field development.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Comparison of protein force fields for molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Automatic atom type and bond type perception in molecular mechanical calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Finishing the euchromatic sequence of the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Development and testing of a general amber force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Size estimation of chemical space: how big is it?

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Good practices in free-energy calculations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Improved treatment of the protein backbone in empirical force fields.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3874408

Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field

3 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24000174

12 December 2020

inferred from PubMed ID database lookup

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24000174

12 December 2020

inferred from PubMed ID database lookup

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24000174

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1002/JCC.23422

1 reference

20 August 2017

journals/jcc/MayneSSTG13

1 reference

DBLP Dataset 2021-01-02

release_2avdqkgsrzbitiszn73lgwt63e

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/2avdqkgsrzbitiszn73lgwt63e

24 November 2022

mapped directly with Wikidata item

PMC publication ID

3874408

1 reference

PMC publication ID

3874408

20 August 2017

PubMed publication ID

24000174

1 reference

PMC publication ID

3874408