Effective knowledge-based potentials (Q30378114)

17 October 2017

Effective knowledge-based potentials (English)

1 reference

17 October 2017

Francisco Melo

2

0 references

author name string

Evandro Ferrada

series ordinal

1

1 reference

17 October 2017

1 July 2009

1 reference

17 October 2017

1 reference

17 October 2017

18

1 reference

17 October 2017

1469-1485

1 reference

17 October 2017

7

1 reference

StAR: a simple tool for the statistical comparison of ROC curves

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Information and discrimination in pairwise contact potentials.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Statistical potential for assessment and prediction of protein 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=2775215

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Measurements of protein sequence-structure correlations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Voro3D: 3D Voronoi tessellations applied to protein 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=2775215

The dependence of all-atom statistical potentials on structural training database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Development of unified statistical potentials describing protein-protein 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=2775215

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Information-theoretic dissection of pairwise contact potentials.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Statistical potentials for fold assessment.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core 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=2775215

Modeling of loops in protein 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=2775215

Filtered neighbors threading.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Influence of protein structure databases on the predictive power of statistical pair potentials

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Assessing protein structures with a non-local atomic interaction energy.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Visible volume: a robust measure for protein structure characterization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Additivity principles in biochemistry

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Recognition of errors in three-dimensional structures of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Protein superfamilies and domain superfolds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

SCOP: a structural classification of proteins database for the investigation of sequences and 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=2775215

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Statistical Mechanical Treatment of Protein Conformation. I. Conformational Properties of Amino Acids in Proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2775215

Information Theory and Statistical Mechanics

20 June 2018

1 reference

Improvement of statistical potentials and threading score functions using information maximization.

21 January 2018

1 reference

Statistical potentials extracted from protein structures: how accurate are they?

21 January 2018

1 reference

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

21 January 2018

1 reference

Cooperativity and the origins of rapid, single-exponential kinetics in protein folding.

21 January 2018

1 reference

Novel knowledge-based mean force potential at atomic level

21 January 2018

1 reference

Local propensities and statistical potentials of backbone dihedral angles in proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19530247

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Helmholtz free energy of peptide hydrogen bonds in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19530247

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Geometric cooperativity and anticooperativity of three-body interactions in native proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19530247

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.166

1 reference

17 October 2017

1 reference

17 October 2017

1 reference

PMCID

2775215