Bioinformatics Vol. 18 no. 1 2002
Pages 140-146
© 2002 Oxford University Press
Concept and prototype of protein–ligand docking simulator with force feedback technology
1 National Cancer Center Research Institute,
5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
2 Tokyo Medical and Dental University,
1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
Received on April 11, 2001
; revised on July 28, 2001
; accepted on September 5, 2001
A novel concept for a protein–ligand docking simulator using Virtual Reality (VR) technologies, in particular the tactile sense technology, was designed and a prototype was developed. Most conventional docking simulators are based on numerical differential calculations of the total energy between a protein and a ligand. However, the basic concept of our method differs from that of conventional simulators. Our design utilizes the force between a ligand and a protein instead of the total energy. The most characteristic function of the system is its ability to enable the user to ‘touch’ and sense the electrostatic potential field of a protein molecule. The user can scan the surface of a protein using a globular probe, which is given an electrostatic charge, and is controlled by a force feedback device. The electrostatic force between the protein and the probe is calculated in real time and immediately fed back into the force feedback device. The user can easily search interactively for positions where the probe is strongly attracted to the force field. Such positions can be regarded as candidate sites where functional groups of ligands corresponding to the probe can bind to the target protein. Certain limitations remain; for example, only twenty protein atoms can be used to generate the electrostatic field. Furthermore, the system can only use globular probes, preventing drug molecules or small chemical groups from being simulated. These limitations are the result of our insufficient computer resources. However, our prototype system has the potential to become a novel application method as well as being applicable to conventional VR technologies, especially to force feedback technologies.
Contact: hi-nagata{at}kddilabs.co.jp; hmizushi{at}ncc.go.jp; tanaka{at}cim.tmd.ac.jp