title: JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs.
abstract: BACKGROUND
  Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs.
  
  
  RESULTS
  JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files.
  
  
  METHODS
  JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported.
  
  
  BACKGROUND
  guillaume.beauclair@inserm.fr
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Beauclair
authors.affiliation: CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and.
authors.forename: Antoine
authors.initials: A
authors.lastname: Bridier-Nahmias
authors.affiliation: Laboratoire Génomique, Bioinformatique, et Applications, EA4627, Chaire de bioinformatique, Conservatoire national des arts et métiers (Cnam), Paris, France.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Zagury
authors.affiliation: CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and.
authors.forename: Ali
authors.initials: A
authors.lastname: Saïb
authors.affiliation: CNRS UMR7212, Hôpital St Louis, Inserm U944, Institut Universitaire d'Hématologie, Hôpital St Louis, Université Paris Diderot, Sorbonne Paris Cité, Hôpital St Louis, Laboratoire PVM, Conservatoire national des arts et métiers (Cnam) and.
authors.forename: Alessia
authors.initials: A
authors.lastname: Zamborlini
mesh_terms: D006801:Humans; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D025841:Small Ubiquitin-Related Modifier Proteins / Q000378:metabolism; D012984:Software; D058207:Sumoylation
chemical_list: D025841:Small Ubiquitin-Related Modifier Proteins