Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes (Q33900447)

29 July 2017

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes (English)

1 reference

29 July 2017

0 references

3

Cecilia Clementi

1 reference

29 July 2017

Payel Das

1

1 reference

PubMed ID

16006532

29 July 2017

Silvina Matysiak

series ordinal

2

1 reference

PubMed ID

16006532

29 July 2017

language of work or name

English

0 references

publication date

8 July 2005

1 reference

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

29 July 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

29 July 2017

102

1 reference

29 July 2017

29

1 reference

29 July 2017

10141-10146

1 reference

COMPUTING: Screen Savers of the World Unite!

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

The effects of nonnative interactions on protein folding rates: theory and simulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Simulation, experiment, and evolution: understanding nucleation in protein S6 folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Intermediates and the folding of proteins L and G.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Orientational potentials extracted from protein structures improve native fold recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

The Jigsaw Puzzle Model: Search for Conformational Specificity in Protein Interiors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Understanding protein folding with energy landscape theory. Part II: Quantitative aspects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Absolute comparison of simulated and experimental protein-folding 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=1177359

The origins of asymmetry in the folding transition states of protein L and protein G.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Unspecific hydrophobic stabilization of folding transition states

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Bergerac-SH3: "frustation" induced by stabilizing the folding nucleus.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Go-ing for the prediction of protein folding mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Prediction of protein-folding mechanisms from free-energy landscapes derived from native 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=1177359

A theoretical search for folding/unfolding nuclei in three-dimensional protein 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=1177359

Protein structure prediction 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=1177359

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 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=1177359

Folding dynamics of the src SH3 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=1177359

Theory of protein folding: the energy landscape perspective

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

How to derive a protein folding potential? A new approach to an old problem

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Evolution-like selection of fast-folding model 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=1177359

5 July 2018

How does a protein fold?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Spin glasses and the statistical mechanics of protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Mapping the transition state and pathway of protein folding by protein engineering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Optimal protein-folding codes from spin-glass theory

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0409471102

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.0409471102

The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0409471102

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0409471102

Switching two-state to three-state kinetics in the helical protein Im9 via the optimisation of stabilising non-native interactions by design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0409471102

Speeding protein folding beyond the G(o) model: how a little frustration sometimes helps

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0409471102

Random-energy model: An exactly solvable model of disordered systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0409471102

Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Structural and energetic consequences of disruptive mutations in a protein core

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1177359

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16006532

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Native and non-native interactions along protein folding and unfolding pathways

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16006532

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0409471102

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference

PubMed ID

16006532