Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures (Q34385674)

1 August 2017

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures (English)

1 reference

1 August 2017

0 references

3

Harold A Scheraga

1 reference

1 August 2017

Jorge A Vila

1

1 reference

PubMed ID

14638943

1 August 2017

Daniel R Ripoll

series ordinal

2

1 reference

PubMed ID

14638943

1 August 2017

language of work or name

English

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publication date

24 November 2003

1 reference

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

1 August 2017

5

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based on heuristic

inferred from page(s)

published in

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1 August 2017

100

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1 August 2017

25

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1 August 2017

14812-14816

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Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

The present view of the mechanism of protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Influence of lysine content and pH on the stability of alanine-based copolypeptides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Atomic detail peptide-membrane interactions: molecular dynamics simulation of gramicidin S in a DMPC bilayer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Protein structure prediction by global optimization of a potential energy function.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Exploring the folding free energy surface of a three-helix bundle protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Molecular dynamics simulations of Leu-enkephalin in water and DMSO.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Toward an outline of the topography of a realistic protein-folding funnel

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Use of buildup and energy-minimization procedures to compute low-energy structures of the backbone of enkephalin.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. III. Probable and average conformations of enkephalin.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine).

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Optimal protocol and trajectory visualization for conformational searches of peptides and proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

The intrinsic helix-forming tendency of L-alanine

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Enkephalin: conformational analysis by means of empirical energy calculations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Use of a Symmetry Condition to Compute the Conformation of Gramicidin S

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=299808

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin.

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

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.2436463100

Folding of a small helical protein using hydrogen bonds and hydrophobicity forces

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

Initial attempts at a theoretical calculation of the conformation of gramicidin-S

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

Conformation of gramicidin S

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

Structure of the type I collagen molecule based on conformational energy computations: the triple-stranded helix and the N-terminal telopeptide

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2436463100

Vibrational analysis of peptides, polypeptides and proteins. XXVII. Structure of gramicidin S from normal mode analyses of low-energy conformations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/14638943

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.2436463100

1 reference

1 August 2017

0 references

1 reference

1 August 2017

1 reference

PubMed ID

14638943