PSAIA - protein structure and interaction analyzer

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. In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein I...

Full description

Saved in:
Bibliographic Details
Published in:BMC structural biology 2008-04, Vol.8 (1), p.21-21, Article 21
Main Authors: Mihel, Josip, Sikić, Mile, Tomić, Sanja, Jeren, Branko, Vlahovicek, Kristian
Format: Article
Language:English
Subjects:
Algorithms
Applications software
Computational Biology
Databases, Protein
Physiological aspects
Protein Binding
Proteins
Proteins - chemistry
Proteins - metabolism
Software
Structure
Structure-activity relationships (Biochemistry)
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. 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. 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.
ISSN:1472-6807
1472-6807
DOI:10.1186/1472-6807-8-21