(Q33493397)

27 July 2017

Four distances between pairs of amino acids provide a precise description of their interaction (English)

1 reference

27 July 2017

Vladimir Potapov

2

0 references

author name string

Mati Cohen

series ordinal

1

1 reference

PubMed ID

19680437

27 July 2017

Gideon Schreiber

series ordinal

3

1 reference

27 July 2017

14 August 2009

1 reference

PLOS Computational Biology

27 July 2017

1 reference

27 July 2017

5

1 reference

27 July 2017

8

1 reference

27 July 2017

e1000470

1 reference

Creative Commons Attribution 4.0 International

27 July 2017

start time

14 August 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Information and discrimination in pairwise contact potentials.

21 June 2018

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

21 June 2018

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A novel empirical free energy function that explains and predicts protein-protein binding affinities.

21 June 2018

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

21 June 2018

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MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes

21 June 2018

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Near-native structure refinement using in vacuo energy minimization.

21 June 2018

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A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures

21 June 2018

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An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure

21 June 2018

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Statistical potential for assessment and prediction of protein structures

21 June 2018

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What is a desirable statistical energy function for proteins and how can it be obtained?

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Potential functions for hydrogen bonds in protein structure prediction and design.

21 June 2018

1 reference

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A new generation of statistical potentials for proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Protein structure evaluation using an all-atom energy based empirical scoring function.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

An atomic environment potential for use in protein structure prediction.

21 June 2018

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Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

21 June 2018

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The modular architecture of protein-protein binding interfaces

21 June 2018

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Development of novel statistical potentials for protein fold recognition

21 June 2018

1 reference

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Protein structure prediction using Rosetta

21 June 2018

1 reference

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PISCES: a protein sequence culling server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Knowledge-based potential functions in protein design.

21 June 2018

1 reference

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Energy estimation in protein design

21 June 2018

1 reference

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Statistical potentials for fold assessment.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

21 June 2018

The Protein Data Bank

1 reference

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Designing potential energy functions for protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

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

21 June 2018

1 reference

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Empirical potentials and functions for protein folding and binding.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Are database-derived potentials valid for scoring both forward and inverted protein folding?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Protein folding by a biased Monte Carlo procedure in the dihedral angle space.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Pseudodihedrals: simplified protein backbone representation with knowledge-based energy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Principles that govern the folding of protein chains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

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

21 June 2018

1 reference

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Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Atomically detailed potentials to recognize native and approximate protein structures.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

A knowledge-based forcefield for protein-protein interface design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Developing optimal non-linear scoring function for protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Can contact potentials reliably predict stability of proteins?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Protein structures from distance inequalities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Prediction of specific protein-DNA recognition by knowledge-based two-body and three-body interaction potentials.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Use of pair potentials across protein interfaces in screening predicted docked complexes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2715887

Novel knowledge-based mean force potential at atomic level

31 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000470

Determinants of side chain conformational preferences in protein structures

21 January 2018

1 reference

12 December 2020

Distance-dependent, pair potential for protein folding: results from linear optimization

1 reference

12 December 2020

Potential of mean force for protein-protein interaction studies

1 reference

12 December 2020

A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000470

Identifiers

DOI

1 reference

journals/ploscb/CohenPS09

27 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

27 July 2017

1 reference

PubMed ID

19680437