Osaka University

Laboratory of Protein Informatics, Research Center for State-of-the-Art Functional Protein Analysis

Institute for Protein Research, Osaka University

English version / Japanese version

Last Updated : 2013.11.11
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New services (MATRAS, GHECOM, KCOMBU) started

Institute for Protein Research

Osaka University


1. Research Goals

Our laboratory, Laboratory of Protein Informatics, is engaged in the protein informatics researches by developing the international protein structural databases and the structural bioinformatics covering molecular modeling and design. We also perform large scale simulation calculations by parallel computers to examine free energy landscapes and biochemical functions of biomolecular systems with molecular dynamics and quantum chemical simulations.

2. Research Activities

Laboratory of Protein Informatics are engaged in the following protein informatics researches:

  1. Development and maintenance of international protein structural databases (PDBj) and structural bioinformatics covering molecular modeling and design.

  2. Development of new databases and Web services: eF-site and eF-seek, for protein surface geometry with the physicochemical properties and search for the similar molecular surfaces; GIRAF for search of ligand binding sites in the PDB that are structurally similar to substructures of the query; HINTdb and HitPredict for databases of homologous protein-protein interactions, and Evolutionary Trace method. We also provide the homology modeling portal, Spanner, and protein-protein docking server, surFit, and we have so far made good remarks at CAPRI contest to predict protein-protein interactions.

  3. Development of new algorithms in statistical physics and chemical physics fields and their applications to large scale simulations with parallel computers and GPGPU for free energy landscapes of protein folding and protein-ligand complex formation. In addition, analyses of biochemical reactions are made with the hybrid QM (Quantum mechanics) / MD (Molecular dynamics) method to reveal the electronic structures of functional sites of proteins.

3. Granted projects in progress
  • Advancement and International Collaboratory for Protein Data Bank at PDBj. Nakamura, H. (BIRD-JST Grants)

4. Computer Facilities
  • PC cluster (Xeon (X5460, Quad Core, 3.16GHz) x 256 CPUs)

  • GPGPU server (NVIDIA Tesla M2050 & M2070: total 28 GPUs)

  • Parallel server with shared memory, Altix UV100 (6 Core Intel Xeon 2.66 GHz x48, 1.5 TB memory) (SGI)

  • File server (SGI Infinite Storage 4100, 96TB)

bIPRbOsaka UniversitybAccess to IPR b
3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN
tel: 06-6879-4311 (Nakamura, Secretary) Fax: 06-6879-8636
Email: (Secretary)