LigDig: A web server for querying ligand-protein interactions

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Abstract

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.

Figures

  • Fig. 1. A workflow showing the modularity of LigDig component tools, what input data they require (green: mandatory, orange: optional), which databases they access (grey), and what output data they produce (cyan). Possibilities to link output data from one tool to another are shown with green arrows from the tool icons.

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CITATION STYLE

APA

Fuller, J. C., Martinez, M., Henrich, S., Stank, A., Richter, S., & Wade, R. C. (2015). LigDig: A web server for querying ligand-protein interactions. Bioinformatics, 31(7), 1147–1149. https://doi.org/10.1093/bioinformatics/btu784

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