(Q35656554)

9 August 2017

title

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta (English)

1 reference

9 August 2017

4

Martin Zacharias

1 reference

9 August 2017

Zhe Zhang

1

1 reference

9 August 2017

Christina E M Schindler

series ordinal

2

1 reference

9 August 2017

Oliver F Lange

series ordinal

3

1 reference

9 August 2017

language of work or name

English

0 references

publication date

8 June 2015

1 reference

9 August 2017

1 reference

9 August 2017

volume

10

1 reference

9 August 2017

issue

6

1 reference

9 August 2017

page(s)

e0125941

1 reference

Creative Commons Attribution 4.0 International

9 August 2017

copyright license

start time

8 June 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Centenary Award and Sir Frederick Gowland Hopkins Memorial Lecture. Protein folding, structure prediction and design.

12 July 2018

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12 July 2018

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

12 July 2018

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An accurate binding interaction model in de novo computational protein design of interactions: if you build it, they will bind

12 July 2018

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Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

12 July 2018

1 reference

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How many protein-protein interactions types exist in nature?

12 July 2018

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Benchmarking and analysis of protein docking performance in Rosetta v3.2.

12 July 2018

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12 July 2018

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Parallel tempering: theory, applications, and new perspectives

12 July 2018

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Convergence and combination of methods in protein-protein docking

12 July 2018

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Minimizing and learning energy functions for side-chain prediction.

12 July 2018

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Protein-protein docking benchmark version 3.0.

12 July 2018

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Estimating the size of the human interactome

12 July 2018

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Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

12 July 2018

1 reference

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High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design

12 July 2018

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High-resolution protein-protein docking

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Prediction and design of macromolecular structures and interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Protein structure prediction using Rosetta

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Protein-protein docking predictions for the CAPRI experiment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

12 July 2018

1 reference

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Free energy landscapes of encounter complexes in protein-protein association

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

From Levinthal to pathways to funnels

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Shape complementarity at protein/protein interfaces

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Docking and scoring protein interactions: CAPRI 2009

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Protein–protein docking benchmark version 4.0

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Hamiltonian replica exchange molecular dynamics using soft-core interactions

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Optimal allocation of replicas in parallel tempering simulations.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Computational redesign of protein-protein interaction specificity

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

Replica Monte Carlo simulation of spin glasses.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4459952

A biased Monte Carlo scheme for zeolite structure solution

25 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0125941

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0125941

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0125941

Feedback-optimized parallel tempering Monte Carlo

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0125941

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0125941

Enhanced Sampling in the Well-Tempered Ensemble

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26053419

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26053419

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0125941

1 reference

release_z27hn47mkrhtflm52vdbaechhe

9 August 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/z27hn47mkrhtflm52vdbaechhe

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

4459952

1 reference

9 August 2017

1 reference