(Q36769352)

16 August 2017

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title

Computational techniques for efficient conformational sampling of proteins (English)

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16 August 2017

computational biology

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4

Harold A Scheraga

1 reference

16 August 2017

1

Adam Liwo

1 reference

16 August 2017

3

Stanisław Ołdziej

1 reference

16 August 2017

2

Cezary Czaplewski

1 reference

16 August 2017

22 January 2008

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Current Opinion in Structural Biology

16 August 2017

1 reference

16 August 2017

18

1 reference

16 August 2017

2

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16 August 2017

134-139

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Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

High accuracy template based modeling by global optimization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Folding pathway of the b1 domain of protein G explored by multiscale modeling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Improved sampling methods for molecular simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

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.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Protein structure prediction by tempering spatial constraints.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Intermediates and the folding of proteins L and G.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Generalized-ensemble algorithms for molecular simulations of biopolymers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Global optimization of clusters, crystals, and biomolecules.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Multicanonical ensemble: A new approach to simulate first-order phase transitions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Self-consistently optimized energy functions for protein structure prediction by molecular dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

A simplified representation of protein conformations for rapid simulation of protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Simulated annealing approach to the study of protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

A knowledge-based move set for protein folding.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Optimized parallel tempering simulations of proteins.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

MONSSTER: a method for folding globular proteins with a small number of distance restraints

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2465814

Generation of accurate protein loop conformations through low-barrier molecular dynamics

5 September 2018

1 reference

12 December 2020

First-principles calculation of the folding free energy of a three-helix bundle protein

1 reference

12 December 2020

All-atom ab initio folding of a diverse set of proteins

1 reference

12 December 2020

Computational studies of ligand diffusion in globins: I. Leghemoglobin

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study

1 reference

12 December 2020

10.1016/J.SBI.2007.12.001

Identifiers

DOI

1 reference

16 August 2017

1 reference

PMC publication ID

2465814

16 August 2017

PubMed publication ID

18215513

1 reference

PMC publication ID

2465814