(Q34731493)

4 August 2017

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

1 reference

4 August 2017

1 reference

1

Michal Brylinski

1 reference

4 August 2017

2

Jeffrey Skolnick

1 reference

PubMed ID

18165317

4 August 2017

language of work or name

English

0 references

publication date

28 December 2007

1 reference

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

4 August 2017

1 reference

4 August 2017

105

1 reference

4 August 2017

129-134

1 reference

4 August 2017

1

1 reference

M-TASSER: an algorithm for protein quaternary structure prediction

4 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Ligation site in proteins recognized in silico.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Blind docking of drug-sized compounds to proteins with up to a thousand residues

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

7 July 2018

The PROSITE database.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

The Universal Protein Resource (UniProt): an expanding universe of protein information

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

TM-align: a protein structure alignment algorithm based on the TM-score

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

GOblet: a platform for Gene Ontology annotation of anonymous sequence data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Automated structure prediction of weakly homologous proteins on a genomic scale

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

A computational pipeline for protein structure prediction and analysis at genome scale.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Ligand binding: functional site location, similarity and docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

THEMATICS: a simple computational predictor of enzyme function from structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Protein structure prediction and structural genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Evolution of function in protein superfamilies, from a structural perspective.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

The Sequence of the Human Genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Defrosting the frozen approximation: PROSPECTOR--a new approach to threading.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Protein structure modeling for structural genomics.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Comparative protein structure modeling of genes and genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Gene ontology: tool for the unification of biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

The genome sequence of Drosophila melanogaster

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

7 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=2224172

KEGG: kyoto encyclopedia of genes and genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Automated analysis of interatomic contacts in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Twilight zone of protein sequence alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Supersites within superfolds. Binding site similarity in the absence of homology.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Comparative protein modelling by satisfaction of spatial restraints

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Flexible ligand docking using a genetic algorithm.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

7 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

A method for localizing ligand binding pockets in protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

Analytical molecular surface calculation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein- and ligand-based virtual screening protocols

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0707684105

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2224172

Practical limits of function prediction

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18165317

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0707684105

1 reference

4 August 2017

0 references

1 reference

4 August 2017

1 reference

PubMed ID

18165317