hrvatski jezikClear Cookie - decide language by browser settings

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

PDF - Published Version - article
Download (1MB) | Preview


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
Project titleProject leaderProject codeProject type
Modeliranje kompleksnih sustavaJeren, Branko036-0362214-1987MZOS
Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritamaTomić, Sanja098-1191344-2860MZOS
Računalna genomika mikrobnih okoliša i bioinformatika ekstremofilaVlahoviček, Kristian119-0982913-1211MZOS
Depositing User: Sanja Tomić
Date Deposited: 09 Apr 2021 12:20
DOI: 10.1186/1472-6807-8-21

Actions (login required)

View Item View Item


Downloads per month over past year

Increase Font
Decrease Font
Dyslexic Font