A force field for virtual atom molecular mechanics of proteins (Q30489864)

19 August 2017

A force field for virtual atom molecular mechanics of proteins (English)

1 reference

19 August 2017

0 references

Anil Korkut

1

1 reference

PMCID

2734882

19 August 2017

Wayne A Hendrickson

series ordinal

2

1 reference

PMCID

2734882

19 August 2017

language of work or name

English

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publication date

28 August 2009

1 reference

Proceedings of the National Academy of Sciences of the United States of America

19 August 2017

1 reference

19 August 2017

106

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19 August 2017

37

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19 August 2017

15667-15672

1 reference

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

OPUS-Ca: a knowledge-based potential function requiring only Calpha positions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Bridging from molecular simulation to biochemical networks.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Near-native structure refinement using in vacuo energy minimization.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Protein structural variation in computational models and crystallographic data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Conformational transitions of adenylate kinase: switching by cracking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Knowledge-based potentials in protein design.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Molecular dynamics: survey of methods for simulating the activity of proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Coarse-grained normal mode analysis in structural biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

EVA: continuous automatic evaluation of protein structure prediction servers.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Anisotropy of fluctuation dynamics of proteins with an elastic network model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Structure of the reovirus core at 3.6 A resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

The crystal structure of the bacterial chaperonin GroEL at 2.8 A

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Cooperative conformational changes in globular proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Computer simulation of protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Proteins in action: the physics of structural fluctuations and conformational changes

28 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Coarse grained protein-lipid model with application to lipoprotein particles

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Anisotropic network model: systematic evaluation and a new web interface.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

A New Method for Coarse-Grained Elastic Normal-Mode Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Protein conformational transitions explored by mixed elastic network models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0907674106

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

Building-block approach for determining low-frequency normal modes of macromolecules.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734882

26 November 2018

Identifiers

DOI

10.1073/PNAS.0907674106

1 reference

19 August 2017

0 references

1 reference

19 August 2017

1 reference

PMCID

2734882