(Q36032595)

11 August 2017

Structure- and sequence-based function prediction for non-homologous proteins (English)

1 reference

protein function prediction

11 August 2017

0 references

protein structure prediction

0 references

3

Daisuke Kihara

1 reference

11 August 2017

Lee Sael

1

1 reference

PMC publication ID

3375349

11 August 2017

Meghana Chitale

series ordinal

2

1 reference

11 August 2017

22 January 2012

1 reference

Journal of Structural and Functional Genomics

11 August 2017

1 reference

11 August 2017

13

1 reference

11 August 2017

2

1 reference

11 August 2017

111-123

1 reference

Constructing patch-based ligand-binding pocket database for predicting function of proteins

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Binding ligand prediction for proteins using partial matching of local surface patches

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

COMBREX: COMputational BRidge to EXperiments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Advances and challenges in protein-ligand docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

TOPSAN: a dynamic web database for structural genomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Real-time ligand binding pocket database search using local surface descriptors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Application of 3D Zernike descriptors to shape-based ligand similarity searching

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The Pfam protein families database

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The Universal Protein Resource (UniProt) in 2010

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

3D-SURFER: software for high-throughput protein surface comparison and analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Improving protein structure similarity searches using domain boundaries based on conserved sequence information.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

ESG: extended similarity group method for automated protein function prediction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Lessons from structural genomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Structure-based function prediction: approaches and applications.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Fast protein tertiary structure retrieval based on global surface shape similarity.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

ConFunc--functional annotation in the twilight zone

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Update on the protein structure initiative.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Characterization of local geometry of protein surfaces with the visibility criterion.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Assessment of predictions submitted for the CASP7 function prediction category.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Function prediction of uncharacterized proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The impact of structural genomics: expectations and outcomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

2 October 2017

The PROSITE database.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Protein molecular function prediction by Bayesian phylogenomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

ProFunc: a server for predicting protein function from 3D structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Metabolomics, genomics, proteomics, and the identification of enzymes and their substrates and products

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Progress of structural genomics initiatives: an analysis of solved target structures.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Enzyme genomics: Application of general enzymatic screens to discover new enzymes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Inference of protein function from protein structure.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The ProDom database of protein domain families: more emphasis on 3D

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

InterPro, progress and status in 2005

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Crystal structure of the YffB protein from Pseudomonas aeruginosa suggests a glutathione-dependent thiol reductase function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The Gene Ontology (GO) database and informatics resource

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

SURFACE: a database of protein surface regions for functional annotation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

GoFigure: automated Gene Ontology annotation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Integrating Structure, Bioinformatics, and Enzymology to Discover Function: BioH, A NEW CARBOXYLESTERASE FROM ESCHERICHIA COLI

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

The Protein Data Bank and structural genomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Electrostatics of nanosystems: application to microtubules and the ribosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

From structure to function: approaches and limitations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

2 October 2017

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=3375349

Combining sensitive database searches with multiple intermediates to detect distant homologues

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Recognition of spatial motifs in protein structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Intermediate sequences increase the detection of homology between sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

SSAP: sequential structure alignment program for protein structure comparison

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Protein structure comparison by alignment of distance matrices

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Protein superfamilies and domain superfolds

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Comparison of spatial arrangements of secondary structural elements in proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Improved tools for biological sequence comparison

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Basic local alignment search tool

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

JAFA: a protein function annotation meta-server

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family

11 July 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Crystal structure and functional characterization of yeast YLR011wp, an enzyme with NAD(P)H-FMN and ferric iron reductase activities

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

New paradigm in protein function prediction for large scale omics analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Protein folds and functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

A new method to detect related function among proteins independent of sequence and fold homology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Identification of the ligand binding sites on the molecular surface of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Inferring functional relationships of proteins from local sequence and spatial surface patterns

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Detection of homologous proteins by an intermediate sequence search

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Conservation of the TRAPPII-specific subunits of a Ypt/Rab exchanger complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

New avenues in protein function prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10969-012-9126-6

Enzyme genomics: Application of general enzymatic screens to discover new enzymes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3375349

21 October 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/22270458

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S10969-012-9126-6

1 reference

11 August 2017

1 reference

PMC publication ID

3375349

11 August 2017

PubMed publication ID

22270458

1 reference

PMC publication ID

3375349