Protein interface classification by evolutionary analysis (Q34520325)

2 August 2017

Protein interface classification by evolutionary analysis (English)

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2 August 2017

1

1 reference

2 August 2017

Adam Srebniak

2

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2 August 2017

Martin A Schärer

series ordinal

3

1 reference

2 August 2017

Guido Capitani

series ordinal

4

1 reference

2 August 2017

22 December 2012

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2 August 2017

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2 August 2017

13

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2 August 2017

334

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describes a project that uses

2 August 2017

PyMOL

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=PMC3556496

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-13-334

0 references

cites work

Immuno- and constitutive proteasome crystal structures reveal differences in substrate and inhibitor specificity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Crystal structure of the channelrhodopsin light-gated cation channel

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

3D ultrastructure of the nuclear pore complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

The real cost of sequencing: higher than you think!

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

The structure of the nuclear pore complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Statistical analysis of interface similarity in crystals of homologous 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=3556496

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

PiQSi: protein quaternary structure investigation.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Inference of macromolecular assemblies from crystalline state

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

A combinatorial score to distinguish biological and nonbiological protein-protein interfaces

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

NOXclass: prediction of protein-protein interaction types

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Conservation and relative importance of residues across protein-protein interfaces

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB 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=3556496

Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE 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=3556496

Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

The Ka/Ks ratio: diagnosing the form of sequence evolution

7 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

7 July 2018

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

Protein structure prediction and structural genomics

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Identification of protein oligomerization states by analysis of interface conservation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

The atomic structure of protein-protein recognition sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Anatomy of hot spots in protein interfaces

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

An evolutionary trace method defines binding surfaces common to protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Principles of protein-protein interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Database of homology-derived protein structures and the structural meaning of sequence alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Conservation helps to identify biologically relevant crystal contacts

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

A dissection of specific and non-specific protein-protein interfaces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

A simple definition of structural regions in proteins and its use in analyzing interface evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

A Putative Mechanism for Downregulation of the Catalytic Activity of the EGF Receptor via Direct Contact between Its Kinase and C-Terminal Domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

Simplified amino acid alphabets for protein fold recognition and implications for folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

Dissecting subunit interfaces in homodimeric proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-334

CASP9 results compared to those of previous CASP experiments

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Analysis and prediction of protein quaternary structure.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Free R value: cross-validation in crystallography

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Protein-protein interfaces: analysis of amino acid conservation in homodimers

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

Discriminating between homodimeric and monomeric proteins in the crystalline state

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3556496

CRK: an evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23259833

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dissecting protein-protein recognition sites

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23259833

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Specific versus non-specific contacts in protein crystals

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23259833

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-13-334

1 reference

journals/bmcbi/DuarteSSC12

2 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

2 August 2017

1 reference