Role of conformational sampling in computing mutation-induced changes in protein structure and stability (Q30399243)

3 November 2017

Role of conformational sampling in computing mutation-induced changes in protein structure and stability (English)

1 reference

3 November 2017

David Baker

3

0 references

Andrew Leaver-Fay

series ordinal

2

object named as

Andrew Leaver-Fay

1 reference

3 November 2017

Elizabeth H Kellogg

1

1 reference

PMCID

3760476

3 November 2017

language of work or name

English

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publication date

3 December 2010

1 reference

3 November 2017

1 reference

3 November 2017

79

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3 November 2017

3

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3 November 2017

830-838

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Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

3 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Macromolecular modeling with rosetta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

High-resolution structure prediction and the crystallographic phase problem

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

The backrub motion: how protein backbone shrugs when a sidechain dances

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Energetic and structural analysis of the role of tryptophan 59 in FKBP12

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

A simple physical model for binding energy hot spots in protein-protein complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Native protein sequences are close to optimal for their structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Effective energy function for proteins in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22921

Eris: an automated estimator of protein stability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22921

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22921

Contributions of the ionizable amino acids to the stability of staphylococcal nuclease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22921

A potential smoothing algorithm accurately predicts transmembrane helix packing.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3760476

Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21287615

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21287615

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting free energy changes using structural ensembles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21287615

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22921

1 reference

3 November 2017

1 reference

3 November 2017

1 reference

PMCID

3760476