(Q30360721)

18 October 2017

WeFold: a coopetition for protein structure prediction (English)

1 reference

protein structure prediction

18 October 2017

0 references

0 references

1 reference

Leandro O Bortot

7

0 references

Gaurav Chopra

Gaurav Chopra

5

0 references

Paweł Krupa

Pawel Krupa

11

0 references

Jaume Bacardit

Jaume Bacardit

6

0 references

David Baker

David Baker

20

0 references

Michael Levitt

25

Michael Levitt

1 reference

18 October 2017

28

Jeffrey Skolnick

1 reference

18 October 2017

27

Harold A Scheraga

1 reference

18 October 2017

2

Adam Liwo

1 reference

18 October 2017

3

Firas Khatib

1 reference

18 October 2017

30

Foldit Players

1 reference

18 October 2017

17

Seth Cooper

1 reference

18 October 2017

1

0 references

James B Smadbeck

15

James Smadbeck

0 references

Christodoulos Floudas

23

Christodoulos A Floudas

0 references

Adam K Sieradzan

14

Adam K Sieradzan

1 reference

18 October 2017

Alexandre C B Delbem

22

1 reference

ORCID Public Data File 2021

Zoran B Popovic

26

Zoran Popović

1 reference

18 October 2017

Magdalena A Mozolewska

13

Magdalena A Mozolewska

1 reference

18 October 2017

16

Tomasz Wirecki

1 reference

18 October 2017

Hongyi Zhou

4

1 reference

18 October 2017

Rodrigo A Faccioli

8

1 reference

18 October 2017

Xin Deng

9

1 reference

18 October 2017

Yi He

10

1 reference

18 October 2017

Jilong Li

12

1 reference

18 October 2017

Jeff Flatten

18

1 reference

18 October 2017

Kefan Xu

19

1 reference

18 October 2017

Jianlin Cheng

21

1 reference

18 October 2017

Chen Keasar

24

1 reference

18 October 2017

Silvia N Crivelli

29

1 reference

18 October 2017

language of work or name

English

0 references

publication date

8 July 2014

1 reference

18 October 2017

1 reference

18 October 2017

82

1 reference

18 October 2017

9

1 reference

18 October 2017

1850-1868

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Critical assessment of methods of protein structure prediction (CASP)--round x

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Assessment of template-free modeling in CASP10 and ROLL.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Protein folding and de novo protein design for biotechnological applications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

CASP10 results compared to those of previous CASP 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=4249725

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Evaluation of predictions in the CASP10 model refinement category.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

GalaxyRefine: Protein structure refinement driven by side-chain repacking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

A large-scale evaluation of computational protein function prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

The protein-folding problem, 50 years on.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

β-sheet topology prediction with high precision and recall for β and mixed α/β proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Assessment of protein structure refinement in CASP9.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Critical assessment of methods of protein structure prediction (CASP)--round IX

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Crystal structure of a monomeric retroviral protease solved by protein folding game players

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

APOLLO: a quality assessment service for single and multiple protein models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Predicting protein structures with a multiplayer online game

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Consistent refinement of submitted models at CASP using a knowledge-based potential

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Improved side-chain torsion potentials for the Amber ff99SB protein force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

MolProbity: all-atom structure validation for macromolecular crystallography

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Selecting high quality protein structures from diverse conformational ensembles.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Assessment of the protein-structure refinement category in CASP8

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Protein structure prediction by pro-Sp3-TASSER.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Solvent dramatically affects protein structure refinement.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Progress and challenges in protein structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Assessment of CASP7 predictions for template-based modeling targets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Ab initio protein structure prediction using chunk-TASSER

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Computational methods in protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Assessing predictions of protein-protein interaction: the CAPRI experiment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Scoring function for automated assessment of protein structure template quality

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Automated structure prediction of weakly homologous proteins on a genomic scale

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Exploring protein native states and large-scale conformational changes with a modified generalized born model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

SPICKER: a clustering approach to identify near-native protein folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

CASP and CAFASP experiments and their findings

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

Comparison of performance in successive CASP 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=4249725

Twilight zone of protein sequence alignments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249725

A large-scale experiment to assess protein structure 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=4249725

The SAMPL2 blind prediction challenge: introduction and overview.

3 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

Addition of side chains to a known backbone with defined side-chain centroids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

The WeFold gateway: Enabling large-scale science coopetition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

Mutation-prediction software rewarded

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24538

Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24677212

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

LINCS: A linear constraint solver for molecular simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.24538

Identifiers

DOI

10.1002/PROT.24538

1 reference

18 October 2017

1 reference

18 October 2017

PubMed publication ID

24677212

1 reference