title: PSAIA - protein structure and interaction analyzer.
abstract: BACKGROUND
  PSAIA (Protein Structure and Interaction Analyzer) was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites.
  
  
  RESULTS
  In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm) for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results.PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format.
  
  
  CONCLUSIONS
  In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.
authors.affiliation: Department of Electronic Systems and Information Processing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, 10000 Zagreb, Croatia. josip.mihel@fer.hr
authors.forename: Josip
authors.initials: J
authors.lastname: Mihel
authors.forename: Mile
authors.initials: M
authors.lastname: Sikić
authors.forename: Sanja
authors.initials: S
authors.lastname: Tomić
authors.forename: Branko
authors.initials: B
authors.lastname: Jeren
authors.forename: Kristian
authors.initials: K
authors.lastname: Vlahovicek
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software
chemical_list: D011506:Proteins