(Q34162840)

31 July 2017

Composite structural motifs of binding sites for delineating biological functions of proteins (English)

1 reference

31 July 2017

2

Haruki Nakamura

1 reference

31 July 2017

Akira R Kinjo

1

1 reference

PubMed ID

22347478

31 July 2017

language of work or name

English

0 references

publication date

8 February 2012

1 reference

31 July 2017

1 reference

31 July 2017

7

1 reference

31 July 2017

2

1 reference

31 July 2017

e31437

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

start time

8 February 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Negative regulation by nuclear receptors: a plethora of mechanisms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Knowledge-based annotation of small molecule binding sites in proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

The overlap of small molecule and protein binding sites within families of protein structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Protein interactions and ligand binding: from protein subfamilies to functional specificity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

FLORA: a novel method to predict protein function from structure in diverse superfamilies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Exploring functional roles of multibinding protein interfaces

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Exploiting structural classifications for function prediction: towards a domain grammar for protein function.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Is protein classification necessary? Toward alternative approaches to function annotation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Protein function prediction--the power of multiplicity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Protein function annotation by homology-based inference

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Comprehensive structural classification of ligand-binding motifs in proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Protein-protein interaction and quaternary structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Architectures and functional coverage of protein-protein interfaces

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

The molecular sociology of the cell

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Inference of macromolecular assemblies from crystalline state

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Growth of novel protein structural data.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Partitioning protein structures into domains: why is it so difficult?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Automated protein function prediction--the genomic challenge

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

SCOPPI: a structural classification of protein-protein interfaces

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

The Universal Protein Resource (UniProt)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

PDBML: the representation of archival macromolecular structure data in XML.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Cytoscape: a software environment for integrated models of biomolecular interaction networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

MATRAS: A program for protein 3D structure comparison

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

CtBP/BARS: a dual-function protein involved in transcription co-repression and Golgi membrane fission

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

A model for statistical significance of local similarities in structure.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Enzyme function less conserved than anticipated.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

28 July 2018

The ACT domain family.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

X-ray crystallographic analyses of complexes between bovine beta-trypsin and Schiff base copper(II) or iron(III) chelates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Protein structure comparison using the markov transition model of evolution.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Three-dimensional structures of glycolate oxidase with bound active-site inhibitors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Molecular structure of flavocytochrome b2 at 2.4 A resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3275580

Dissection study on the severe acute respiratory syndrome 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Lessons from structural genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Docking by structural similarity at protein-protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Proteome-wide prediction of overlapping small molecule and protein binding sites using structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Structure-function correlation in glycine oxidase from Bacillus subtilis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Crystal structure of human factor VIIa/tissue factor in complex with peptide mimetic inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Structural basis of DNA recognition by p53 tetramers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

The generation of new protein functions by the combination of domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Protein structural change upon ligand binding correlates with enzymatic reaction mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Classification and annotation of the relationship between protein structural change and ligand binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Structural comparison of F1-ATPase: interplay among enzyme structures, catalysis, and rotations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

PQS: a protein quaternary structure file server

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

eF-site and PDBjViewer: database and viewer for protein functional sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

PPiClust: EFFICIENT CLUSTERING OF 3D PROTEIN–PROTEIN INTERACTION INTERFACES

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0031437

Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22347478

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22347478

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22347478

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0031437

1 reference

31 July 2017

0 references

0 references

1 reference

31 July 2017

1 reference

PubMed ID

22347478