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Updated: May 26, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Docking-calculation-based method for predicting protein-RNA interactions
Masahito Ohue1, Yuri Matsuzaki, Yutaka Akiyama
1Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan. ohue@bi.cs.titech.ac.jp
Abstract:
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.
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