PSAIA - Protein Structure and Interaction Analyzer

Mihel, Josip; Šikić, Mile; Tomić, Sanja; Jeren, Branko; Vlahoviček, Kristian (2008) PSAIA - Protein Structure and Interaction Analyzer. BMC STRUCTURAL BIOLOGY, 8 . ISSN 1472-6807

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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.

Item Type:

Article

Uncontrolled Keywords:

protein interaction ; accessible surface area ; depth index ; protrusion index ;

Subjects:

NATURAL SCIENCES > Biology

Divisions:

Division of Organic Chemistry and Biochemistry

Projects:

Project title	Project leader	Project code	Project type
Modeliranje kompleksnih sustava	Jeren, Branko	036-0362214-1987	MZOS
Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama	Tomić, Sanja	098-1191344-2860	MZOS
Računalna genomika mikrobnih okoliša i bioinformatika ekstremofila	Vlahoviček, Kristian	119-0982913-1211	MZOS