LigDig: a web server for querying ligand-protein interactions.

Jonathan C Fuller,Rebecca C Wade,Stefan Henrich,Michael Martinez,Antonia Stank,Stefan Richter

doi:10.1093/bioinformatics/btu784

Abstract

Summary: 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.Contact: jonathan.fuller@h-its.org, rebecca.wade@h-its.orgSupplementary information: Supplementary data are available at Bioinformatics online.

Highlights

There has been growing discussion of the ‘data deluge’ and the perceived problems surrounding it, namely how to store, process and visualize data, and how to combine multiple heterogeneous data sources
For many working in the cross-disciplinary environment of systems biology research, the challenge of combining these data sources can be great, but the rewards of doing so can be even greater
LigDig was developed to assist a user with a set of example questions that might be encountered in a typical systems biology

Summary

Introduction

There has been growing discussion of the ‘data deluge’ and the perceived problems surrounding it, namely how to store, process and visualize data, and how to combine multiple heterogeneous data sources. Tools to assist the modeling of biochemical networks, such as SYCAMORE (Weidemann et al, 2008) or MetNetMaker (Forth et al, 2010), can simplify the construction of metabolic models, most require knowledge of database identifiers for the biological entities of interest. Such tools show the utility of integrating data from several sources and simplifying the handling of multiple database identifiers. LigDig uses the strategy of accessing multiple data sources and assisting the user to interpret results that might not be possible by visiting a single data source alone. LigDig assists users in performing basic manipulations of protein structures that can help researchers to gain new insights into their system of interest

Design

Examples

Which proteins does my ligand inhibit and why?