(Q37589571)

21 August 2017

Three-body interactions improve the prediction of rate and mechanism in protein folding models (English)

1 reference

21 August 2017

0 references

M R Ejtehadi

1

1 reference

21 August 2017

S P Avall

series ordinal

2

1 reference

21 August 2017

S S Plotkin

series ordinal

3

1 reference

21 August 2017

language of work or name

English

0 references

publication date

6 October 2004

1 reference

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

21 August 2017

1 reference

21 August 2017

101

1 reference

21 August 2017

42

1 reference

21 August 2017

15088-15093

1 reference

Simulations of the role of water in the protein-folding mechanism

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

The fast protein folding problem

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

The present view of the mechanism of protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Absolute comparison of simulated and experimental protein-folding dynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Understanding protein folding with energy landscape theory. Part I: Basic concepts

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

De novo design of biocatalysts

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Protein folding theory: from lattice to all-atom models

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Ab initio protein structure prediction: progress and prospects.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Three key residues form a critical contact network in a protein folding transition state

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

A combined algorithm for genome-wide prediction of protein function

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Experiment and theory highlight role of native state topology in SH3 folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Mapping the interactions present in the transition state for unfolding/folding of FKBP12.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Designing potential energy functions for protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Contact order, transition state placement and the refolding rates of single domain proteins.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Local interactions and the optimization of protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

From Levinthal to pathways to funnels

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

On the origin of the cooperativity of protein folding: implications from model simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Dominant forces in protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Navigating the folding routes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Co-operative interactions during protein folding.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Protein Folding: A Perspective from Theory and Experiment.

25 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

How do small single-domain proteins fold?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Protein folding funnels: the nature of the transition state ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Three-body correlations in protein folding: the origin of cooperativity

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

A breakdown of symmetry in the folding transition state of protein L

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0403486101

Interpreting the folding kinetics of helical proteins

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=524050

Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity

3 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15469920

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15469920

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15469920

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0403486101

1 reference

21 August 2017

0 references

1 reference

1 reference

21 August 2017

PubMed publication ID

15469920

1 reference