Folding helical proteins in explicit solvent using dihedral-biased tempering (Q35991691)

11 August 2017

Folding helical proteins in explicit solvent using dihedral-biased tempering (English)

1 reference

Correction for Zhang and Ma, Folding helical proteins in explicit solvent using dihedral-biased tempering

11 August 2017

0 references

corrigendum / erratum

0 references

author name string

Cheng Zhang

series ordinal

1

1 reference

PMCID

3361456

11 August 2017

Jianpeng Ma

series ordinal

2

1 reference

PMCID

3361456

11 August 2017

language of work or name

English

0 references

publication date

9 May 2012

1 reference

11 August 2017

6

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

1 reference

11 August 2017

109

1 reference

11 August 2017

21

1 reference

11 August 2017

8139-8144

1 reference

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

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

How fast-folding proteins fold

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Carbon monoxide poisoning is prevented by the energy costs of conformational changes in gas-binding haemproteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Atomic-level characterization of the structural dynamics of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Enhanced sampling and applications in protein folding in explicit solvent

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Structural Insights into Serine-rich Fimbriae from Gram-positive Bacteria

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Common structural transitions in explicit-solvent simulations of villin headpiece folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Direct single-molecule observation of a protein living in two opposed native structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Solution structure and sugar-binding mechanism of mouse latrophilin-1 RBL: a 7TM receptor-attached lectin-like domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Mutations as trapdoors to two competing native conformations of the Rop-dimer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

The protein folding problem: when will it be solved?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Canonical sampling through velocity rescaling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

The protein folding 'speed limit'.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

The present view of the mechanism of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Structure of a de novo designed protein model of radical enzymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

De novo design of proteins--what are the rules?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Structure of a conserved domain common to the transcription factors TFIIS, elongin A, and CRSP70

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

The solution structure of oxidized Escherichia coli cytochrome b562

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Solution structure and dynamics of a de novo designed three-helix bundle protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Theory of protein folding: the energy landscape perspective

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Simulation via direct computation of partition functions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

From coiled coils to small globular proteins: design of a native-like three-helix bundle

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

27 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Rate constant and reaction coordinate of Trp-cage folding in explicit water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Replica-exchange method using the generalized effective potential.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha3W--a large-scale Monte Carlo study.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

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/10.1073%2FPNAS.1112143109

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1112143109

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3361456

New Monte Carlo technique for studying phase transitions

23 September 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Balance between α and β Structures in Ab Initio Protein Folding

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1112143109

1 reference

11 August 2017

0 references

1 reference

11 August 2017

1 reference

PMCID

3361456