Molecular dynamics is a computational technique used to simulate a dynamic behavior of a molecule based on Newton’s equation of motion which parameters are interactions between atoms in a molecule.

This new server reduces processing time of molecular dynamics simulation with a dedicated computation board “MD Engine^®” that processes time-consuming computation, nonbonded interactions at high speed. This server is highly suited for new drug development.

Screening of candidate drug that affects target protein using simulation, such as the molecular dynamics (MD) simulation, is more important, instead of the conventional method using experimental screening. However, its use had been limited to the basic researches since determining molecular structure of target protein and estimating interactions between protein and candidate drug require a vast amount of computation time ranging from days to months. “MD Engine^®” is specialized in high-speed processing of programs dedicated for molecular dynamics simulation, and achieves high price/performance. NEC will actively develop solutions to promote new (in silico) drug discovery aided by computer simulation.

Simulation time has been dramatically reduced by an embedded “MD Engine^®,” a dedicated computation board for high-speed computation of nonbonded interactions such as coulomb force and intermolecular force that account for more than 99% in many cases of molecular dynamics simulation. It realizes as approximately 340 times as fast speed compared to MD computation (*3) on a conventional PC server.

Calculation on a molecule can be done with high accuracy because nonbonded interactions can be calculated without cutoff; a method of omitting a calculation of nonbonded interactions between long distance atoms, which is normally applied to reduce the computation time. This restrains the outbreak of simulation errors such as decomposition of molecule or illegal conformation during the calculation.

The server supports AMBER, which is a standard molecular dynamics simulation program, and provides its post-processing tool (sold separately). This tool enables users to execute programs on the MD Server from a client PC, and shows the results on the graphic display. In addition, the dedicated library function empowers the user’s original molecular dynamics programs.

All the MD Server-related developments including standard programs such as AMBER, a dedicated board and a library, are conducted by NEC. Worldwide support system and more than 400 of maintenance centers domestically, which is the largest number in the industry, are available to support users. They also provide technical support in applying the MD Server to users’ original molecular dynamic programs.

The new product’s hardware price starts at 3,400,000 yen(28,432 US$) for the smallest configuration. The shipping starts on November 30, 2005. NEC expects 1,500 system sales in next three years.

Post-genome research such as determining structure of protein and unraveling reaction mechanism is cast a spotlight on, after the completion of decoding of the human genome. Especially. developing new drugs that affects target protein is strongly promoted by pharmaceutical industry. This development has been done by experimental method through a trial and error process. However, to reduce a period and cost, many industries try to introduce in silico drug discovery system. This is a computing system to efficiently supplement the conventional in vivo (in the living body) and in vitro (in an artificial environment) studies. Based on 3D structures of polymer such as protein, it predicts the way of bonding (docking mode) and degree of attractive forces (affinity) between protein and prospective drug chemical compounds.