(Q36926799)

17 August 2017

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

1 reference

17 August 2017

X-ray crystallography

0 references

author name string

Mingyang Lu

series ordinal

1

1 reference

17 August 2017

Jianpeng Ma

series ordinal

2

1 reference

17 August 2017

language of work or name

English

0 references

publication date

1 October 2008

1 reference

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

17 August 2017

1 reference

17 August 2017

105

1 reference

17 August 2017

40

1 reference

17 August 2017

15358-15363

1 reference

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

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics 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=2563068

Normal-Mode Refinement of Anisotropic Thermal Parameters for Potassium Channel KcsA at 3.2 Å Crystallographic Resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Protein structural variation in computational models and crystallographic data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

The Amber biomolecular simulation programs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Coarse-grained normal mode analysis in structural biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

The role of shape in determining molecular motions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Quantifying allosteric effects in proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular 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=2563068

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Development and testing of a general amber 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=2563068

New advances in normal mode analysis of supermolecular complexes and applications to structural refinement

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Force fields for protein 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=2563068

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

How to describe protein motion without amino acid sequence and atomic coordinates.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Anisotropy of fluctuation dynamics of proteins with an elastic network 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=2563068

Effective energy function for proteins in solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Dynamics of a small globular protein in terms of low-frequency vibrational modes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Refinement of protein dynamic structure: normal mode refinement

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

vGNM: a better model for understanding the dynamics of proteins in crystals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

oGNM: online computation of structural dynamics using the Gaussian Network 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=2563068

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Folding of small helical proteins assisted by small-angle X-ray scattering profiles.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

The origin and extent of coarse-grained regularities in protein internal packing

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2563068

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

4 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0806072105

On Information and Sufficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0806072105

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0806072105

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0806072105

Computing a nearest symmetric positive semidefinite matrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0806072105

Allostery in a coarse-grained model of protein dynamics

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18832168

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Coarse-graining of protein structures for the normal mode studies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18832168

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0806072105

1 reference

release_4k344qgpzzbbvag7yhftu2mbr4

17 August 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/4k344qgpzzbbvag7yhftu2mbr4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

17 August 2017

1 reference