Protein structure prediction using basin-hopping. (Q30369969)

18 August 2017

Protein structure prediction using basin-hopping. (English)

1 reference

protein structure prediction

18 August 2017

0 references

3

Peter G Wolynes

1 reference

18 August 2017

Michael C Prentiss

1

1 reference

PMCID

2674628

18 August 2017

David J Wales

series ordinal

2

1 reference

PMCID

2674628

18 August 2017

language of work or name

English

0 references

publication date

1 June 2008

1 reference

Journal of Chemical Physics

18 August 2017

1 reference

18 August 2017

128

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18 August 2017

22

1 reference

18 August 2017

225106

1 reference

Toward high-resolution prediction and design of transmembrane helical protein structures

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Water mediation in protein folding and molecular recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta 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=2674628

SimFold energy function for de novo protein structure prediction: consensus with Rosetta.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Scalable molecular dynamics with NAMD

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

GROMACS: fast, flexible, and free

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Water 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=2674628

Associative memory Hamiltonians for structure prediction without homology: alpha/beta 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=2674628

The Bioperl toolkit: Perl modules for the life sciences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Associative memory hamiltonians for structure prediction without homology: alpha-helical 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=2674628

3 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Global optimization of clusters, crystals, and biomolecules.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Clustering of low-energy conformations near the native structures of small 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=2674628

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Self-consistently optimized statistical mechanical energy functions for sequence structure alignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Theoretical Studies of Protein Folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Conformation of Polypeptides and 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=2674628

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Generalized protein tertiary structure recognition using associative memory Hamiltonians.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Optimal protein-folding codes from spin-glass theory

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Improvements in the prediction of protein backbone topography by reduction of statistical errors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674628

Toward protein tertiary structure recognition by means of associative memory hamiltonians.

3 June 2018

1 reference

Random-energy model: An exactly solvable model of disordered systems

21 January 2018

1 reference

Optimizing physical energy functions for protein folding.

21 January 2018

1 reference

Global optimization and folding pathways of selected alpha-helical proteins.

21 January 2018

1 reference

Protein Structure Prediction: The Next Generation.

21 January 2018

1 reference

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

21 January 2018

1 reference

Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach

21 January 2018

1 reference

Basin hopping simulations for all-atom protein folding

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18554063

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18554063

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.2929833

1 reference

18 August 2017

1 reference

1 reference

18 August 2017

1 reference

PMCID

2674628