Evol and ProDy for bridging protein sequence evolution and structural dynamics (Q34136883)

24849577

31 July 2017

title

Evol and ProDy for bridging protein sequence evolution and structural dynamics (English)

1 reference

31 July 2017

0 references

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Timothy R. Lezon

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

author name string

Ahmet Bakan

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Anindita Dutta

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Ying Liu

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Chakra Chennubhotla

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Ivet Bahar

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

language of work or name

English

0 references

publication date

21 May 2014

1 reference

24849577

31 July 2017

number of pages

3

1 reference

based on heuristic

inferred from page(s)

published in

Bioinformatics

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

volume

30

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

issue

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

page(s)

2681-2683

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones

4 June 2020

cites work

1 reference

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Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments

28 July 2018

1 reference

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Collective dynamics differentiates functional divergence in protein evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Sequence evolution correlates with structural dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Protein 3D structure computed from evolutionary sequence variation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

ProDy: protein dynamics inferred from theory and experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Global dynamics of proteins: bridging between structure and function

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Structural and functional constraints in the evolution of protein families

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Protein sectors: evolutionary units of three-dimensional structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Protein dynamism and evolvability.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Biopython: freely available Python tools for computational molecular biology and bioinformatics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Influence of naturally-occurring 5â ²-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: An X-ray crystallographic study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Identification of direct residue contacts in protein-protein interaction by message passing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

ET viewer: an application for predicting and visualizing functional sites in protein structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

PDB file parser and structure class implemented in Python

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Essential dynamics of proteins

28 July 2018

1 reference

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Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction

21 January 2018

1 reference

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Anisotropic network model: systematic evaluation and a new web interface

21 January 2018

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Probing the diverse landscape of protein flexibility and binding

21 January 2018

1 reference

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155247

Harmonicity in slow protein dynamics

28 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU336

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24849577

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTU336

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/BakanDMLCLB14

4 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_khhezyftmzck3c6x52vwt4dyre

28 January 2021

Fatcat ID

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Fatcat

https://api.fatcat.wiki/v0/release/khhezyftmzck3c6x52vwt4dyre

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

24849577

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24849577%20AND%20SRC:MED&resulttype=core&format=json