RSS21 Revolutionary Simulation Software
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All-Electron Based Simulation System for Protein Reactions; the New Infrastructural Bio-Medicinal Technology

ProteinDF system enables the world’s largest all-electron calculation on proteins by density functional theory

Associate Professor Fumitoshi SATO
Information Technology Center / Institute of Industrial Science
The University of Tokyo

Associate Professor Fumitoshi SATO

We are developing the high-quality simulation system for protein reaction based on all-electron calculation by density functional method program, ProteinDF. Through proof calculations the simulation method is developed to a firm technology. The followings are integrated to construct the system.

(1) Development of All-Electron Calculation Engine on Super-large-scale Proteins by Density Functional Method

To perform all-electron calculation on almost all the proteins registered in PDB(http://www.rcsb.org/pdb/ ), we are tuning the ProteinDF engine. The rate-limiting routines are extracted and parallelized to achieve high efficiency so that it can correspond to computers of 1000 CPUs. The technique of the automatic calculation is also investigated.

(2) Development of Structural Optimization, Molecular Dynamics and Free Energy Calculation

The high-speed structural optimization, the molecular dynamics and the free energy calculation methods are developed to estimate the intermolecular interaction in the protein system precisely.

(3) Construction of Protein Wavefunction Database

We are constructing the protein wavefunction database. It links with the genetic information databases and PDB.

(4) Development of High-Quality GUI to Support and Analyze All Simulations and the Physical Properties

We develop GUI(Graphical User Interface) for the simulation system of protein reaction based on all-electron calculation. It supports the methods to perform structural modeling for drug design, link with database, and express new physical properties.

GUI sample

The Electrostatic potential map on the isoelectronic surface of Insulin hexamer. The number of residues, atoms and orbitals are 306, 4,716 and 26,766, respectively. This calculation is the world record of the scale of the density functional method.

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