A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD [article]

Imran S Haque, Kyle A Beauchamp, Vijay S Pande
2014 bioRxiv   pre-print
The bottleneck for the rapid calculation of the root-mean-square deviation in atomic coordinates (RMSD) between pairs of protein structures for large numbers of conformations is the evaluation of a (3xN) x (Nx3) matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3xN case that are able to significantly outperform (by up to 3X) off- the-shelf high-performance linear algebra libraries for this computation, reaching machine limits on
more » ... . The routines are implemented in C and Python libraries, and are available at https://github.com/simtk/IRMSD.
doi:10.1101/008631 fatcat:ihxoepv6fnbevi4ofmvhcsq4fq