DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction (Q29038132)

27 March 2017

Drena Dobbs

4

0 references

Vasant Honavar

5

object named as

Vasant Honavar

1 reference

27 March 2017

author name string

Li C. Xue

1

1 reference

27 March 2017

Rafael A. Jordan

2

1 reference

27 March 2017

EL-Manzalawy Yasser

3

1 reference

27 March 2017

language of work or name

English

0 references

publication date

17 October 2013

1 reference

27 March 2017

1 reference

27 March 2017

volume

82

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27 March 2017

issue

2

1 reference

27 March 2017

page(s)

250-267

1 reference

Docking and scoring protein complexes: CAPRI 3rd Edition

27 March 2017

cites work

1 reference

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Inference of macromolecular assemblies from crystalline state

6 April 2017

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

6 April 2017

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

6 April 2017

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Diversity of protein-protein interactions

6 April 2017

1 reference

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

6 April 2017

1 reference

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Principles of docking: An overview of search algorithms and a guide to scoring functions

6 April 2017

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6 April 2017

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

6 April 2017

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

6 April 2017

1 reference

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HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

6 April 2017

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Assessing the accuracy of prediction algorithms for classification: an overview

7 April 2017

1 reference

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Predicting protein-protein interface residues using local surface structural similarity

7 April 2017

1 reference

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Protein-protein docking and hot-spot prediction for drug discovery.

9 May 2017

1 reference

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Constructing structural networks of signaling pathways on the proteome scale

3 June 2018

1 reference

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Protein docking prediction using predicted protein-protein interface

3 June 2018

1 reference

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Partner-aware prediction of interacting residues in protein-protein complexes from sequence data

3 June 2018

1 reference

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DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

3 June 2018

1 reference

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Protein-protein complex structure predictions by multimeric threading and template recombination

3 June 2018

1 reference

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Integrating atom-based and residue-based scoring functions for protein-protein docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

HomPPI: a class of sequence homology based protein-protein interface prediction methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Transient protein-protein interactions.

3 June 2018

1 reference

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A collaborative filtering approach for protein-protein docking scoring functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

3 June 2018

1 reference

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Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Structural interpretation of protein-protein interaction network

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Pushing structural information into the yeast interactome by high-throughput protein docking experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Progress and challenges in predicting protein-protein interaction sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Convergence and combination of methods in protein-protein docking

3 June 2018

1 reference

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A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

3 June 2018

1 reference

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Protein-protein interaction and quaternary structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

How proteins get in touch: interface prediction in the study of biomolecular complexes.

3 June 2018

1 reference

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Protein-protein docking benchmark version 3.0.

3 June 2018

1 reference

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M-TASSER: an algorithm for protein quaternary structure prediction

3 June 2018

1 reference

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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

3 June 2018

1 reference

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Combination of scoring schemes for protein docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

High-throughput identification of interacting protein-protein binding sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Interaction-site prediction for protein complexes: a critical assessment

3 June 2018

1 reference

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Relating three-dimensional structures to protein networks provides evolutionary insights

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Protein binding site prediction using an empirical scoring function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

GRAMM-X public web server for protein-protein docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Optimised amino acid specific weighting factors for unbound protein docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

WHISCY: what information does surface conservation yield? Application to data-driven docking.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Structure, function, and evolution of transient and obligate protein-protein interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

ClusPro: a fully automated algorithm for protein-protein docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Prediction of functional sites by analysis of sequence and structure conservation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Structural characterisation and functional significance of transient protein-protein interactions

3 June 2018

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Interactome3D: adding structural details to protein networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24370

Assessment of blind predictions of protein-protein interactions: current status of docking methods

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24370

Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24370

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

ZRANK: reranking protein docking predictions with an optimized energy function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Protein docking using surface matching and supervised machine learning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Funnel hunting in a rough terrain: learning and discriminating native energy funnels.

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24370

ProMate: a structure based prediction program to identify the location of protein-protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Using protein binding site prediction to improve protein docking

21 January 2018

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https://api.crossref.org/works/10.1002%2FPROT.24370

A new protein-protein docking scoring function based on interface residue properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Docking and scoring protein interactions: CAPRI 2009

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

meta-PPISP: a meta web server for protein-protein interaction site prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Prediction of protein interaction sites from sequence profile and residue neighbor list

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Development and testing of an automated approach to protein docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Principles of docking: An overview of search algorithms and a guide to scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24370

Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

Use of pair potentials across protein interfaces in screening predicted docked complexes.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417613

RDOCK: Refinement of rigid‐body protein docking predictions

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23873600

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24370

1 reference