Prediction of protein-protein complex structures

Eiji Kanamori, Yoichi Murakami, Joy Sarmiento, Shide Uang, Daron M. Standley, Matsuyuki Shirota, Kengo Kinoshita, Yuko Tsucillya, Junicill Higo, Haruki Nakamura

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)


A docking method, surFit, was developed that automatically and semi-automatically docks a pair of protein molecular surfaces. It performs the following six procedures: Binding site prediction, Rigid surface docking, Coarse scoring, Refinement, Precise scoring, and Re-rejinement by molecular dynamics.rimldotion. The first four procedures have been automated and implemented in the webscrver surFit. The current protocol successfully built many acceptable predicted complex structures with high qualities for the recent CAPRI targets, and accurately estimated the solvent water positions at the interface for CAPRI Target 47. To reveal the complex structure of an intrinsically disordered protein (IDP) with its partner receptor protein, enhanced sampling computations were performed to simulate the free energy landscapes of the IDP with and without the receptor. Consequently, both induced fitting and population shift mechanisms were observed for the NRSF-Sin3 system.

Original languageEnglish
Title of host publicationBiomolecular Forms and Functions
Subtitle of host publicationA Celebration of 50 Years of the Ramachandran Map
PublisherWorld Scientific Publishing Co.
Number of pages13
ISBN (Electronic)9789814449144
ISBN (Print)9789814449137
Publication statusPublished - 2012 Jan 1

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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