LigDig: a web server for querying ligand–protein interactions

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Background: One of the major challenges in complex multi-disciplinary systems biology projects is to understand and process data from a wide variety of data sources. Computational tools to assist in the analysis of this data are essential.
Method: 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.
Results: 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.
Conclusion: LigDig is designed to be amenable to use by non-experts in bio- and chemo-informatics. A typical user of the LigDig webserver might be a systems biology researcher building signaling or metabolic network models who needs to disambiguate compound names or make use of structural information on protein-ligand binding. LigDig is available at: http://mcm.h-its.org/ligdig

Filename: Poster_Stank.pdf

Format: PDF document

Size: 1.24 MB

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

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Stefan Henrich, Stefan Richter

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Views: 648    Downloads: 169
  • Created: 15th Jan 2016 at 13:49
  • Last used: 22nd Mar 2018 at 01:15

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