(Q34768244)

4 August 2017

title

ΔΔPT: a comprehensive toolbox for the analysis of protein motion (English)

1 reference

Thomas Charles Buckland McLeish

4 August 2017

author

7

1 reference

4 August 2017

Martin J Cann

5

0 references

Thomas L. Rodgers

object named as

Thomas L Rodgers

1

0 references

Mark R. Wilson

object named as

Mark R Wilson

6

0 references

Ehmke Pohl

object named as

Ehmke Pohl

4

0 references

author name string

David Burnell

2

1 reference

4 August 2017

Phil D Townsend

3

1 reference

4 August 2017

language of work or name

1 reference

7 June 2013

1 reference

4 August 2017

1 reference

4 August 2017

volume

14

1 reference

4 August 2017

page(s)

183

1 reference

Creative Commons Attribution 2.0 Generic

4 August 2017

copyright license

start time

7 June 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

ProDy: protein dynamics inferred from theory and experiments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Normal mode analysis and applications in biological physics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Computational identification of slow conformational fluctuations in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

An elastic network model of HK97 capsid maturation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Dynamical properties of the MscL of Escherichia coli: a normal mode analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Normal mode analysis with simplified models to investigate the global dynamics of biological systems.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Conformational change of proteins arising from normal mode calculations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

7 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Knowledge-based protein secondary structure assignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Normal modes as refinement parameters for the F-actin model

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

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

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

Real-space refinement with DireX: from global fitting to side-chain improvements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

Comparative normal mode analysis of LFA-1 integrin I-domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

Dynamic interaction among the platform domain and two membrane-proximal immunoglobulin-like domains of class I major histocompatibility complex: normal mode analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

FlexServ: an integrated tool for the analysis of protein flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

Structural flexibility in proteins: impact of the crystal environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Analysis of domain motions by approximate normal mode calculations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

Hinge-bending motion in citrate synthase arising from normal mode calculations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689072

How Does KCNE1 Regulate the Kv7.1 Potassium Channel? Model-Structure, Mutations, and Dynamics of the Kv7.1-KCNE1 Complex

26 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-14-183

Dynamic character of human growth hormone and its receptor: normal mode analysis

21 January 2018

1 reference

12 December 2020

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

1 reference

12 December 2020

Analysis of domain motions in large proteins

1 reference

12 December 2020

Normal mode analysis of G-actin

1 reference

12 December 2020

Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures

1 reference

12 December 2020

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-14-183

1 reference

journals/bmcbi/RodgersBTPCWM13

4 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

4 August 2017

1 reference