Introduction

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. CONCLUSION: 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.

Publications

  1. PSAIA - protein structure and interaction analyzer.
    Cite this
    Mihel J, Sikić M, Tomić S, Jeren B, Vlahovicek K, 2008-01-01 - BMC structural biology

Credits

  1. Josip Mihel
    Developer

  2. Mile Šikić
    Developer

  3. Sanja Tomić
    Developer

  4. Branko Jeren
    Developer

  5. Kristian Vlahoviček
    Investigator

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Summary
AccessionBT006614
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByKristian Vlahoviček