RT Journal Article
SR Electronic
T1 RUPEE: A fast and accurate purely geometric protein structure search
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 475301
DO 10.1101/475301
A1 Ronald Ayoub
A1 Yugyung Lee
YR 2018
UL http://biorxiv.org/content/early/2018/11/20/475301.abstract
AB Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. We have developed RUPEE, a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles.Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results.The RUPEE protein structure search is available at http://www.ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.