Environment-dependent residue contact energies for proteins. (Q30326368)

3 September 2017

Environment-dependent residue contact energies for proteins. (English)

1 reference

3 September 2017

C Zhang

1

1 reference

3 September 2017

S H Kim

series ordinal

2

1 reference

3 September 2017

language of work or name

English

0 references

publication date

1 March 2000

1 reference

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

3 September 2017

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3 September 2017

97

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3 September 2017

6

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3 September 2017

2550-2555

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Detection of protein fold similarity based on correlation of amino acid properties

3 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Effective use of sequence correlation and conservation in fold recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Protein secondary structure prediction based on position-specific scoring matrices

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Designing potential energy functions for protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Determinants of strand register in antiparallel beta-sheets of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Theory of protein folding: the energy landscape perspective

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Protein fold recognition by prediction-based threading

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Determination of atomic desolvation energies from the structures of crystallized proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Protein topology recognition from secondary structure sequences: application of the hidden Markov models to the alpha class proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Coordination geometry of nonbonded residues in globular proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

From Levinthal to pathways to funnels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Structure-derived potentials and protein simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Protein fold recognition by mapping predicted secondary structures.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Prediction of protein secondary structure at better than 70% accuracy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

A simplified representation of protein conformations for rapid simulation of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

The Protein Data Bank: a computer-based archival file for macromolecular structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

MONSSTER: a method for folding globular proteins with a small number of distance restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

Removing near-neighbour redundancy from large protein sequence collections

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

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.040573597

The dependence of amino acid pair correlations on structural environment.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=15966

Context is a major determinant of β-sheet propensity

26 November 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

Extracting contact energies from protein structures: a study using a simplified model

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.040573597

21 January 2018

Identifiers

DOI

10.1073/PNAS.040573597

1 reference

release_ytwgydodtnhzbon3dyg5glbocq

3 September 2017

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1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ytwgydodtnhzbon3dyg5glbocq

mapped directly with Wikidata item

24 November 2022

based on heuristic

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3 September 2017

1 reference