title: SCDFinder, a web-based tool for the identification of putative novel ATM and ATR targets.
abstract: BACKGROUND
  The S/TQ cluster domain (SCD) constitutes a new type of protein domain that is not defined by sequence similarity but by the presence of multiple S/TQ motifs within a variable stretch of amino acids. SCDs are recognized targets for DNA damage response (DDR) kinases like ATM and ATR. Characterizing DDR targets is of significant interest. The aim of this work was to develop a web-based tool to allow for easy identification and visualization of SCDs within specific proteins or in whole proteome sets, a feature not supported by current domain and motif search tools.
  
  
  RESULTS
  We have developed an algorithm that (i) generates a list of all proteins in an organism containing at least one user-defined SCD within their sequence, or (ii) identifies and renders a visual representation of all user-defined SCDs present in a single sequence or batch of sequences.
  
  
  METHODS
  The application was developed using Pearl and Python, and is available at the following URL: http://ustbioinfo.webfactional.com/scd/.
authors.affiliation: Department of Mathematics, Computer Science and Cooperative Engineering, University of St. Thomas and Bioinformatics Program, Department of Biology, University of St. Thomas, 3800 Montrose Blvd, Houston, TX, 77006 USA.
authors.forename: Lukas
authors.initials: L
authors.lastname: Cara
authors.affiliation: Department of Mathematics, Computer Science and Cooperative Engineering, University of St. Thomas and Bioinformatics Program, Department of Biology, University of St. Thomas, 3800 Montrose Blvd, Houston, TX, 77006 USA.
authors.forename: Medina
authors.initials: M
authors.lastname: Baitemirova
authors.affiliation: Department of Mathematics, Computer Science and Cooperative Engineering, University of St. Thomas and Bioinformatics Program, Department of Biology, University of St. Thomas, 3800 Montrose Blvd, Houston, TX, 77006 USA.
authors.forename: Franklin
authors.initials: F
authors.lastname: Duong
authors.affiliation: Department of Mathematics, Computer Science and Cooperative Engineering, University of St. Thomas and Bioinformatics Program, Department of Biology, University of St. Thomas, 3800 Montrose Blvd, Houston, TX, 77006 USA.
authors.forename: Maia
authors.initials: M
authors.lastname: Larios-Sanz
authors.affiliation: Department of Mathematics, Computer Science and Cooperative Engineering, University of St. Thomas and Bioinformatics Program, Department of Biology, University of St. Thomas, 3800 Montrose Blvd, Houston, TX, 77006 USA.
authors.forename: Albert
authors.initials: A
authors.lastname: Ribes-Zamora
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D064007:Ataxia Telangiectasia Mutated Proteins / Q000378:metabolism*; D030562:Databases, Protein; D020407:Internet; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D020543:Proteome; D064007:Ataxia Telangiectasia Mutated Proteins