Docking-calculation-based method for predicting protein-RNA interactions.
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.
Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan. ohue@bi.cs.titech.ac.jp
Masahito
M
Ohue
Yuri
Y
Matsuzaki
Yutaka
Y
Akiyama
D000595:Amino Acid Sequence; D001483:Base Sequence; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software
D016601:RNA-Binding Proteins; D012313:RNA