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LigDig: a web server for querying ligand-protein interactions

Abstract:

Summary: LigDig is a webserver 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 chemo-informatics. LigDig is available at: http://mcm.h-its.org/ligdig

Contact: mcmsoft{at}h-its.org

Supplementary Information: Design features of the LigDig tools are available at Bioinformatics online.

10.1093/bioinformatics/btu784

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., F3: Kinetic data handling

Bioinformatics
Bioinformatics
29th Nov 2014

J. C. Fuller, M. Martinez, S. Henrich, A. Stank, S. Richter, R. C. Wade

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[Jonathan Fuller] [Michael Martinez] [Rebecca Wade]

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Cell
Views: 1651
  • Created: 6th Dec 2014 at 18:03
  • Last updated: 6th Dec 2014 at 18:07

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