Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins (Q35146195)

6 August 2017

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins (English)

1 reference

6 August 2017

Jed W Pitera

1

1 reference

PubMed ID

12808142

6 August 2017

William Swope

series ordinal

2

1 reference

PubMed ID

12808142

6 August 2017

language of work or name

English

0 references

publication date

13 June 2003

1 reference

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

6 August 2017

1 reference

6 August 2017

100

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6 August 2017

13

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6 August 2017

7587-7592

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

6 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Absolute comparison of simulated and experimental protein-folding dynamics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Native-like mean structure in the unfolded ensemble of small proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Designing a 20-residue protein

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

The free energy landscape for beta hairpin folding in explicit water

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Exendin-4 and glucagon-like-peptide-1: NMR structural comparisons in the solution and micelle-associated states

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Generalized-ensemble algorithms for molecular simulations of biopolymers

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Folding simulations of a three-stranded antiparallel beta -sheet peptide

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

13 July 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=164630

Folding dynamics and mechanism of beta-hairpin formation

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Contacting the protein folding funnel with NMR.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Stability of proteins: small globular proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

Reversible peptide folding in solution by molecular dynamics simulation.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=164630

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

27 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1330954100

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1330954100

Blue Gene: A vision for protein science using a petaflop supercomputer

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1330954100

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1330954100

Molecular dynamics study of peptides in implicit water: ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif

21 January 2018

1 reference

12 December 2020

Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

12 December 2020

Exploring the energy landscape of a beta hairpin in explicit solvent

1 reference

12 December 2020

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1330954100

1 reference

6 August 2017

0 references

1 reference

6 August 2017

1 reference

PubMed ID

12808142