LigDig: a web server for querying ligand-protein interactions.
Bioinformatics
; 31(7): 1147-9, 2015 Apr 01.
Article
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| MEDLINE
| ID: mdl-25433696
ABSTRACT
UNLABELLED LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein-ligand complexes. The LigDig webserver is modular in design and consists of seven tools, which can be used separately, or via linking the output from one tool to the next, in order to answer more complex questions. Currently, the tools allow a user to (i) perform a free-text compound search, (ii) search for suitable ligands, particularly inhibitors, of a protein and query their interaction network, (iii) search for the likely function of a ligand, (iv) perform a batch search for compound identifiers, (v) find structures of protein-ligand complexes, (vi) compare three-dimensional structures of ligand binding sites and (vii) prepare coordinate files of protein-ligand complexes for further calculations. AVAILABILITY AND IMPLEMENTATION LigDig makes use of freely available databases, including ChEMBL, PubChem and SABIO-RK, and software programs, including cytoscape.js, PDB2PQR, ProBiS and Fconv. LigDig can be used by non-experts in bio- and chemoinformatics. LigDig is available at http//mcm.h-its.org/ligdig. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
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Proteínas
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Internet
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2015
Tipo del documento:
Article