DARON M. STANDLEY, Ph.D.

JST Researcher, Protein Data Bank Japan (PDBj)

Guest Associate Professor, Center for Advanced

Medical Engineering and Informatics (MEI Center), Osaka University

Institute for Protein Research (IPR), Osaka University,

3-2 Yamadaoka, Suita, Osaka, Japan 565-0871

TEL: +81-(0)6-6879-4311

FAX: +81-(0)6-6879-8636

Research Interests

I am currently working on the following collaborative projects at the Laboratory of Functional Informatics, headed by Prof. Haruki Nakamura (IPR):

Protein structure-based queries. As part of the PDBj project, and in collaboration with Prof. Hiroyuki Toh (Medical Institute of Bioregulation, Kyushu University), we are developing Structure Navigator, an efficient and robust protein structure search engine.

Functional annotation. We are developing methods to assign putative functions to newly solved structural genomics (SG) targets based on primary and tertiary structural similarity to functionally characterized protein families. As a preliminary test of the method we are focusing on hypothetical proteins from the Protein 3000 project that have been deposited to and released from the PDB.

Flexible protein-protein docking. We are using restrained molecular dynamics (MD) to study amyloid fibril formation in b₂-microglobulin, in collaboration with Prof. Yuji Goto (IPR) and Dr. Narutoshi Kamiya (MEI Center).

Flexible protein-ligand docking. In collaboration with Dr. Mark van der Giezen, University of Exeter, we are using flexible ligand docking and MD to understand nucleotide specificity in succinyl-CoA synthetase.

Development of new protein-protein docking methods. In collaboration Prof. Kengo Kinoshita (Human Genome Center, Institute of Medical Science, University of Tokyo), we are developing novel docking methods and testing them in the CAPRI docking experiment.

Publications