Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment (Q30387414)

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3 April 2020

title

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment (English)

1 reference

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3 April 2020

101

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3 April 2020

Marc F. Lensink

1

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3 April 2020

Sameer Velankar

2

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3 April 2020

Andriy Kryshtafovych

3

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Joan Segura

7

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3 April 2020

Narcis Fernandez-Fuentes

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3 April 2020

Emilie Neveu

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David W. Ritchie

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3 April 2020

Marie-Dominique Devignes

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3 April 2020

Mieczyslaw Torchala

26

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3 April 2020

Paul A. Bates

28

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3 April 2020

Raphaël Guérois

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Anna Vangone

39

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João Pglm Rodrigues

40

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Panagiotis L. Kastritis

47

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Alexandre Bonvin

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Xianjin Xu

49

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3 April 2020

Yang Shen

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Yang Shen

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Neil J Bruce

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Iain H Moal

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Shourya S Roy Burman

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Jeffrey J. Gray

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100

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17

Lim Heo

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18

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Hasup Lee

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Koen Visscher

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Thom Vreven

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author name string

Shen-You Huang

4

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Shruthi Viswanath

9

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Ron Elber

10

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Sergei Grudinin

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Petr Popov

12

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Sangwoo Park

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Sanbo Qin

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Huan-Xiang Zhou

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Bernard Maigret

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Raphaël A G Chaleil

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Ilya A Vakser

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Jooyoung Lee

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Sandor Vajda

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Tanggis Bohnuud

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Nicholas Marze

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3 April 2020

Edrisse Chermak

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Andrey Tovchigrechko

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Andrej Sali

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Miriam Eisenstein

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Jinchao Yu

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language of work or name

English

0 references

publication date

1 June 2016

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3 April 2020

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3 April 2020

volume

84 Suppl 1

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page(s)

323-348

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Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

3 April 2020

cites work

1 reference

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Blind prediction of interfacial water positions in CAPRI

20 June 2018

1 reference

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20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

High-resolution comparative modeling with RosettaCM.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Intertwined associations in structures of homooligomeric proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Biochemistry. Integrative structural biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Computational design of novel protein binders and experimental affinity maturation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Trendspotting in the Protein Data Bank

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Protein structure prediction from sequence variation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Template-based protein structure modeling using the RaptorX web server.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Templates are available to model nearly all complexes of structurally characterized proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

HexServer: an FFT-based protein docking server powered by graphics processors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

The HADDOCK web server for data-driven biomolecular docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Proteome organization in a genome-reduced bacterium

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Evaluation of template-based models in CASP8 with standard measures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Fast and accurate automatic structure prediction with HHpred.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Convergence and combination of methods in protein-protein docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

The RosettaDock server for local protein-protein docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Recent Progress and Future Directions in Protein-Protein Docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Docking and scoring protein complexes: CAPRI 3rd Edition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Inference of macromolecular assemblies from crystalline state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

TM-align: a protein structure alignment algorithm based on the TM-score

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Protein homology detection by HMM-HMM comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

LGA: A method for finding 3D similarities in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Structural basis of macromolecular recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

20 June 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=5030136

Processing and evaluation of predictions in CASP4

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Structural symmetry and protein function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

Comparative protein modelling by satisfaction of spatial restraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5030136

The cell as a collection of protein machines: preparing the next generation of molecular biologists

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.25007

Docking and scoring protein interactions: CAPRI 2009.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.25007

M-ZDOCK: a grid-based approach for Cn symmetric multimer docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.25007

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.25007

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.25007

Blind predictions of protein interfaces by docking calculations in CAPRI.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.25007

The subunit interfaces of weakly associated homodimeric proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27122118

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural biology. Beyond blob-ology

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27122118

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.25007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27122118%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27122118%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

1 reference