Moldyn method speeds up molecular modeling

17 Jun 2002

A new approach to molecular dynamics modeling developed by Moldyn Inc. (Cambridge, MA) with co-funding from NIST's Advanced Technology Program, produces simulations of molecular movements and properties 100 times faster than conventional methods.

The new technique relies on substructuring, which organizes groups of similarly behaving atoms into interacting flexible bodies, to dramatically cut the number of calculations needed to estimate the behavior of large molecules such as proteins. The method was adapted from aerospace modeling techniques used to account for forces on hundreds of thousands of parts in spacecraft and satellites.

Conventional, atom-by-atom, molecular dynamics programs can require weeks to months to calculate the behavior of a few molecules. Moldyn's "multibody" approach subdivides a large molecule into a few interacting bodies to generate simulations that show excellent agreement with all-atom-based methods but that can be produced much more quickly. The multibody method already has been tested with a pharmaceutical modeling program to help improve the realism of drug/protein interaction simulations. Drug companies use databases containing hundreds of thousands to millions of different molecules and molecule fragments to look for potential medicines. Moldyn's software may allow more efficient screening of these large databases to find molecules that can dock successfully with the active sites on proteins.