(Q34979501)

5 August 2017

title

Replica exchange improves sampling in low-resolution docking stage of RosettaDock (English)

1 reference

5 August 2017

Zhe Zhang

1

1 reference

5 August 2017

Oliver F Lange

series ordinal

2

1 reference

5 August 2017

language of work or name

English

0 references

publication date

29 August 2013

1 reference

5 August 2017

1 reference

5 August 2017

volume

8

1 reference

5 August 2017

issue

8

1 reference

5 August 2017

page(s)

e72096

1 reference

Creative Commons Attribution 4.0 International

5 August 2017

copyright license

start time

29 August 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Alternate states of proteins revealed by detailed energy landscape mapping

8 July 2018

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

8 July 2018

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Protein-protein docking dealing with the unknown

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Convergence and combination of methods in protein-protein docking

8 July 2018

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United we stand: combining structural methods

8 July 2018

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Replica exchange simulations of transient encounter complexes in protein-protein association.

8 July 2018

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Recent Progress and Future Directions in Protein-Protein Docking

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Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization

8 July 2018

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The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

8 July 2018

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8 July 2018

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POPSCOMP: an automated interaction analysis of biomolecular complexes

8 July 2018

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

8 July 2018

1 reference

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Diversity of protein-protein interactions

8 July 2018

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Protein-protein docking with a reduced protein model accounting for side-chain flexibility

8 July 2018

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8 July 2018

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Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3756964

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3756964

Prediction of protein-protein interactions by docking methods.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3756964

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3756964

Next challenges in protein-protein docking: from proteome to interactome and beyond

8 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Quantitative use of chemical shifts for the modeling of protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Scoring optimisation of unbound protein-protein docking including protein binding site predictions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Predictive docking of protein-protein and protein-DNA complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

ZDOCK: an initial-stage protein-docking algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

ICM-DISCO docking by global energy optimization with fully flexible side-chains

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Geometry-based flexible and symmetric protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Docking and scoring protein interactions: CAPRI 2009

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

A temperature predictor for parallel tempering simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Optimal allocation of replicas in parallel tempering simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0072096

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24009670

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein docking using continuum electrostatics and geometric fit

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24009670

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0072096

1 reference

5 August 2017

0 references

1 reference

5 August 2017

1 reference