(Q37601847)

21 August 2017

How good is automated protein docking? (English)

1 reference

21 August 2017

0 references

Dima Kozakov

1

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author name string

Dmitri Beglov

2

1 reference

21 August 2017

Tanggis Bohnuud

3

1 reference

21 August 2017

Scott E Mottarella

4

1 reference

21 August 2017

Bing Xia

5

1 reference

21 August 2017

David R Hall

6

1 reference

21 August 2017

Sandor Vajda

7

1 reference

21 August 2017

language of work or name

English

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publication date

17 October 2013

1 reference

21 August 2017

1 reference

21 August 2017

81

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21 August 2017

12

1 reference

21 August 2017

2159-2166

1 reference

Sampling and scoring: a marriage made in heaven

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Structural basis of bacterial defense against g-type lysozyme-based innate immunity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Application of asymmetric statistical potentials to antibody-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Structure of the ultra-high-affinity colicin E2 DNase--Im2 complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

The HADDOCK web server for data-driven biomolecular docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Accounting for conformational changes during protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Convergence and combination of methods in protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

The RosettaDock server for local protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Docking and scoring protein complexes: CAPRI 3rd Edition

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

PatchDock and SymmDock: servers for rigid and symmetric docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Optimal clustering for detecting near-native conformations in protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

ClusPro: a fully automated algorithm for protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

CAPRI: a Critical Assessment of PRedicted Interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Efficient computational algorithms for docking and for generating and matching a library of functional epitopes I. Rigid and flexible hinge-bending docking algorithms.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Clustering of low-energy conformations near the native structures of small proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Modelling protein docking using shape complementarity, electrostatics and biochemical information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

SwarmDock and the use of normal modes in protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

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

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

GRAMM-X public web server for protein-protein docking

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Docking and scoring protein interactions: CAPRI 2009.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

ClusPro: performance in CAPRI rounds 6-11 and the new server.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Identification of near-native structures by clustering protein docking conformations.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

PIPER: an FFT-based protein docking program with pairwise potentials.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

A protein-protein docking benchmark.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

ZDOCK: an initial-stage protein-docking algorithm.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Protein docking using spherical polar Fourier correlations.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

Low-resolution docking: prediction of complexes for underdetermined structures.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934018

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

1 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24403

Protein docking using continuum electrostatics and geometric fit

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23996272

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24403

1 reference

21 August 2017

1 reference

21 August 2017

PubMed publication ID

23996272

1 reference