Section: New Software and Platforms

MD-Kmean

Keywords: Molecular Dynamics Analysis

Scientific Description

MD-Kmean is a fast program for the analysis of large numbers of Molecular Dynamics frames. The accurate comparison of different protein structures plays important roles in structural biology, structure prediction and functional annotation. The root-mean-square-deviation (RMSD) after optimal superposition is the predominant measure of similarity due to the ease and speed of computation. MD-Kmean was designed to perform both the RMSD and the clustering step necessary to compare large numbers of protein 3D structures stored in large datasets and was applied to a set of 2 microsecond MD simulations producing 2 million frames to be compared and clustered.

Functional Description

We have implemented a very fast version of RMSD for graphics processing units (GPUs) using a quaternion method for calculating the optimal superposition and RMSD that is designed for parallel applications. This acceleration in speed allows RMSD calculations to be used efficiently in computationally intensive applications such as the clustering of large number of molecular dynamics frames. MD-Kmean is 50 times faster on a Nvidia GPU, on average, than the original single-threaded CPU implementation on an Intel quad-core processor.

• Contact: Bernard Maigret