About PoSSuM


Today, vast amounts of protein-small molecule binding sites are available in the Protein Data Bank (PDB). Comprehensive comparisons are computationally demanding, but will be useful for prediction of protein functions and drug discovery. We proposed a tremendously fast algorithm called "SketchSort" that makes it possible to enumerate similar pairs in a huge number of binding sites. We applied the proposed method to all-pair similarity searches for 5.5 million known and potential binding sites , and discovered over 49 million similar pairs of binding sites.
  The result was compiled as a relational database Pocket Similarity Search using Multiple-Sketches (PoSSuM), which includes all the discovered pairs with annotations of various types (e.g., UniProt, CATH, SCOP, SCOPe, EC number and Gene ontology). PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar folds. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures. Basically, the users can search similar binding pockets using three search modes:

i) "Search K" is useful for finding similar binding sites for a known ligand-binding site. Post a known ligand-binding site (a pair of "PDB ID" and "HET code") in the PDB, and PoSSuM will search similar sites for the query site.

ii) "Search P" is useful for predicting ligands that potentially bind to a structure of interest. Post a known protein structure (PDB ID) in the PDB, and PoSSuM will search similar known-ligand binding sites for the query structure.

iii) "Drug Search" is useful for retrieving ligand analogs and investigating receptor diversity. User can choose a query ligand from a list of approved small-compound drugs, then PoSSuM will show its ligand analogs and potential recepors.




Latest release


15-Oct-2014

Major improvement: a new servce called PoSSuM Drug Search (PoSSuMds) has been released

11-Sept-2014

Minor improvements have been implemented: 3D molecular viewer was switched from Jmol to JSmol

11-Sept-2014

Minor improvements have been implemented: display representative pairs

10-Sept-2014

The latest version of dataset has been released, which includes up-to-date PDB entries (ver May-2014).

24-Apr-2014

Minor improvements have been implemented: download superposed coordinates

23-Aug-2013

Minor improvements have been done including sorting table, superposition viewer, etc

21-Jun-2013

The latest version of dataset has been released, which includes up-to-date PDB entries (ver Jan-2013).

21-June-2013

The latest version of dataset has been released, which includes up-to-date PDB entries (ver Jan-2013).

28-Mar-2012

The latest version of dataset has been released, which includes up-to-date PDB entries (ver Jan-2012).

22-Dec-2011

The latest version of dataset has been released. Almost all PDB entries (67,212) have been used for generating putative pockets in the current version, whereas the older version included only 29,779 entries (95% sequence similarity cut-off).

1-Nov-2011

Online calculation mode (Beta version) has been released. Users can upload their protein structure of interest, in case the structure has not been deposited to PDB.




The PoSSuM database is freely available for all researchers. Please cite the following papers:

  1. Ito J, Ikeda K, Yamada K, Mizuguchi K, Tomii K. PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res. DB issue 2015;43:D392-8.

  2. Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K. PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. DB issue 2012;40:D541-8.

  3. Ito J, Tabei Y, Shimizu K, Tomii K, Tsuda K. PDB-Scale analysis of known and putative ligand binding sites with structural sketches. Proteins 2011;80:747-63.

  4. Tabei Y, Uno T, Sugiyama M, Tsuda K. Single Versus Multiple Sorting for All Pairs Similarity Search. The 2nd Asian Conference on Machine Learning (ACML2010) 2010.

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