TY - JOUR T1 - A Fast 3 × <em>N</em> Matrix Multiply Routine for Calculation of Protein RMSD JF - bioRxiv DO - 10.1101/008631 SP - 008631 AU - Imran S. Haque AU - Kyle A. Beauchamp AU - Vijay S. Pande Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/09/02/008631.abstract N2 - 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 3 × N × N × 3 matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3 × N 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 performance. The routines are implemented in C and Python libraries, and are available at https://github.com/simtk/IRMSD. ER -