(Q34977466)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

title

Protein binding site prediction using an empirical scoring function (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

protein function prediction

28 December 2019

main subject

0 references

author

Chi Zhang

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

Yaoqi Zhou

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

author name string

Shide Liang

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

Song Liu

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

language of work or name

English

0 references

publication date

7 August 2006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

volume

34

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

page(s)

3698-3707

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

issue

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

Structural systems biology: modelling protein interactions.

28 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Structure, function, and evolution of transient and obligate protein-protein interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

A structural perspective on protein-protein interactions.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Protein interaction networks from yeast to human

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of functional sites by analysis of sequence and structure conservation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Insufficiently dehydrated hydrogen bonds as determinants of protein interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Side-chain conformational entropy at protein-protein interfaces.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of functionally important residues based solely on the computed energetics of protein structure.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Conservation of polar residues as hot spots at protein interfaces.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

8 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

The atomic structure of protein-protein recognition sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Analysis of protein-protein interaction sites using surface patches

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Bayesian statistical analysis of protein side-chain rotamer preferences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

An evolutionary trace method defines binding surfaces common to protein families

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Principles of protein-protein interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

A role for surface hydrophobicity in protein-protein recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Amino acid substitution matrices from protein blocks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Exploiting sequence and structure homologs to identify protein-protein binding sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Statistical analysis and prediction of protein-protein interfaces

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Improved prediction of protein-protein binding sites using a support vector machines approach.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Distinguishing structural and functional restraints in evolution in order to identify interaction sites.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

ProMate: a structure based prediction program to identify the location of protein-protein binding sites

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Effective scoring function for protein sequence design.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

A protein-protein docking benchmark.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Assessment of blind predictions of protein-protein interactions: current status of docking methods.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of protein--protein interaction sites in heterocomplexes with neural networks.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of protein interaction sites from sequence profile and residue neighbor list.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Residue frequencies and pairing preferences at protein-protein interfaces.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Prediction of protein-protein interaction sites using patch analysis.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1540721

Analysis of the steric strain in the polypeptide backbone of protein molecules

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16893954

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural clusters of evolutionary trace residues are statistically significant and common in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16893954

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL454

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16893954%20AND%20SRC:MED&resulttype=core&format=json

28 December 2019

1 reference