title: LigDig: a web server for querying ligand-protein interactions.
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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
authors.forename: Jonathan C
authors.initials: JC
authors.lastname: Fuller
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Martinez
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Henrich
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
authors.forename: Antonia
authors.initials: A
authors.lastname: Stank
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Richter
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Wade
mesh_terms: D001665:Binding Sites; D016208:Databases, Factual; D005635:Fructosediphosphates / Q000378:metabolism; D006801:Humans; D020407:Internet; D008024:Ligands; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
chemical_list: D005635:Fructosediphosphates; D008024:Ligands; D011506:Proteins; C029063:fructose-1,6-diphosphate