university lille north of france LigASite database of binding sites
You can download the LigASite database in XML format:
Or, if you just want the XML Schema:
(XML files for individual proteins can be found at their respective pages)
Furthermore, we also provide the core data of LigASite in a comma-separated file. The format of this file is:
  • field 1: apo PDB ID
  • field 2: residue type and position of binding site residue
  • field 3: a hyphen-separated list of holo PDB ID's in which the residue is found in contact with a ligand.
Note that the XML files contain the detailed information describing all binding sites in the dataset (e.g. list of protein atoms in contact with HET-groups, list of HET-groups considered relevant, etc.).
The comma-separated version is created from the XML file.
Previous versions of LigASite are available for download here.
(v9.4; March 2011)  A few HETATM amino acid residues were erroneously included in binding site descriptions in a small number of entries in LigASite. This issue accounted for a total of 23 residues distributed across 13 entries in LigASite v9.3. The problem has been resolved from LigASite v9.4 onwards. Please contact the authors if you require a list of erroneous residues in previous versions of LigASite.
(v9.0; September 2010)  LigASite now uses PISA instead of PQS to define quaternary structures, as the latter service was discontinued in August 2009.
(v7.0; March 2009)  Due to a problem in the LigASite update procedure, some entries in the non-redundant (nr25) datasets in fact share more than 25% sequence identity. This issue has been resolved from version 7.0 onward. Please contact us if you need correct lists of non-redundant entries for any of the earlier LigASite updates.
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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