(Q33849857)

29 July 2017

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

1 reference

29 July 2017

0 references

3

Harold A Scheraga

1 reference

29 July 2017

1

Adam Liwo

1 reference

29 July 2017

Mey Khalili

2

1 reference

PubMed ID

15677316

29 July 2017

language of work or name

English

0 references

publication date

26 January 2005

1 reference

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

29 July 2017

1 reference

29 July 2017

102

1 reference

29 July 2017

2362-2367

1 reference

29 July 2017

7

1 reference

The protein folding problem: global optimization of the force fields.

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

The protein folding 'speed limit'.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

All-atom simulations of protein folding and unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

TOUCHSTONE: a unified approach to protein structure prediction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Funnel sculpting for in silico assembly of secondary structure elements of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Structure of a de novo designed protein model of radical enzymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Long time dynamics of complex systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Folding funnels: the key to robust protein structure prediction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Protein folding and unfolding at atomic resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Structural analysis of WW domains and design of a WW prototype

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Calculation of protein conformation by global optimization of a potential energy function.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Solution structure of the albumin-binding GA module: a versatile bacterial protein domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Contact potential that recognizes the correct folding of globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Computing time scales from reaction coordinates by milestoning.

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408885102

Optimizing physical energy functions for protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408885102

A mezoscopic model of nucleic acids. Part 1. Lagrangian and quaternion molecular dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408885102

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408885102

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408885102

Toward minimalist models of larger proteins: a ubiquitin-like protein

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548970

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

29 October 2018

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

Thermal folding and mechanical unfolding pathways of protein secondary structures

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0408885102

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference

PubMed ID

15677316