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A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD
[article]
2014
bioRxiv
pre-print
Preserved Fulltext
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
doi:10.1101/008631
fatcat:ihxoepv6fnbevi4ofmvhcsq4fq