DOCKING-CALCULATION-BASED METHOD FOR PREDICTING PROTEIN-RNA INTERACTIONS

• Published in: Genome Informatics Vol. 25; no. 1; pp. 25 - 39
• Main Authors: AKIYAMA, YUTAKA, OHUE, MASAHITO, MATSUZAKI, YURI
• Format: Journal Article
• Language: English
• Published: Japan Japanese Society for Bioinformatics 2011; 日本バイオインフォマティクス学会
• Subjects: all-to-all prediction; Amino Acid Sequence; Base Sequence; Data banks; Data processing; FFT-based rigid-body docking; Informatics; Molecular Docking Simulation; Molecular Sequence Data; Protein Binding; Protein structure; protein-RNA interaction; RNA - chemistry; RNA - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism; Software; Tertiary structure
• ISSN: 0919-9454; 2185-842X
• DOI: 10.11234/gi.25.25

Elucidating protein-RNA interactions (PRIs) is important for understanding many cellular systems. We developed a PRI prediction method by using a rigid-body protein-RNA docking calculation with tertiary structure data. We evaluated this method by using 78 protein-RNA complex structures from the Protein Data Bank. We predicted the interactions for pairs in 78×78 combinations. Of these, 78 original complexes were defined as positive pairs, and the other 6,006 complexes were defined as negative pairs; then an F-measure value of 0.465 was obtained with our prediction system.