(Q28389605)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

title

Recent Developments and Applications of the CHARMM force fields (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

author name string

Xiao Zhu

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

Pedro E M Lopes

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

language of work or name

English

0 references

publication date

28 June 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

Wiley Interdisciplinary Reviews: Computational Molecular Science

10 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

volume

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

page(s)

167-185

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

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

10 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

CHARMM: the biomolecular simulation program

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Development of an empirical force field for silica. Application to the quartz-water interface

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Scalable molecular dynamics with NAMD

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Solvent interactions determine carbohydrate conformation

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Dynamics of folded proteins

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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=3468154

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

The Cambridge Structural Database: a quarter of a million crystal structures and rising

7 April 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

7 April 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Toward a consensus view of duplex RNA flexibility

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Targeting of an interrupted polypurine:polypyrimidine sequence in mammalian cells by a triplex-forming oligonucleotide containing a novel base analogue

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Many-body polarization effects and the membrane dipole potential

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Intrinsic curvature properties of photosynthetic proteins in chromatophores

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Additive empirical force field for hexopyranose monosaccharides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Automated conformational energy fitting for force-field development.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Are current molecular dynamics force fields too helical?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Understanding the dielectric properties of liquid amides from a polarizable force field.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Molecular dynamics simulations of nucleic acid-protein complexes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Empirical force fields for biological macromolecules: overview and issues.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Protein simulation and drug design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Development and current status of the CHARMM force field for nucleic acids.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

29 September 2017

Polarizable force fields

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Three-dimensional structures of oligosaccharides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Potential energy functions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Free energy profile of RNA hairpins: a molecular dynamics simulation study

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

A molecular mechanics model for imatinib and imatinib:kinase binding

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

The Water Dipole Moment in Water Clusters

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Cholesterol flip-flop: insights from free energy simulation studies

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

How does proteinase 3 interact with lipid bilayers?

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Polarization and polarizability assessed by protein amide acidity

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Importance of accurate DNA structures in solution: the Jun-Fos model

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Improved treatment of the protein backbone in empirical force fields.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

Modern protein force fields behave comparably in molecular dynamics simulations

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3468154

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

27 November 2018

1 reference

12 December 2020

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

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

Molecular dynamics investigation of psalmopeotoxin I. Probing the relationship between 3D structure, anti-malarial activity and thermal stability

1 reference

12 December 2020

Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

1 reference

12 December 2020

Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments

1 reference

12 December 2020

Special Issue on Polarization

1 reference

12 December 2020

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

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

A revised potential-energy surface for molecular mechanics studies of carbohydrates

1 reference

12 December 2020

Identifiers

DOI

10.1002/WCMS.74

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2403856

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

OpenCitations bibliographic resource ID

10 March 2020

2403856

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json

10 March 2020

PubMed publication ID

23066428

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23066428%20AND%20SRC:MED&resulttype=core&format=json