RUPEE: A fast and accurate purely geometric protein structure search
By Ronald Ayoub, Yugyung Lee. 2018
41 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Computational Biology & Bioinformatics
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Lisa N. Kinch
- Andriy Kryshtafovych
- Nick V. Grishin
- Dustin R Schaeffer
- Yang Zhang
- Bohdan Monastyrskyy
- Torsten Schwede
- Krzysztof Fidelis
In Computational Biology & Bioinformatics
- Nick V. Grishin
- Lisa N. Kinch
- Andriy Kryshtafovych
- Dustin R Schaeffer
- Yang Zhang
- Krzysztof Fidelis
- Badri Adhikari
- Jianlin Cheng
Citations in the corpus
- Target Classification in the 14th Round of the Critical Assessment of Protein Structure Prediction (CASP14). (2021, methodology): “To aid in homology and topology-level assignments, top structure-based templates from the PDB were identified using structure coordinates of complete targets and split EUs using LGA,22 Dalilite,24 and RUPEE.32 Structure-based templates without significant sequence relationship or other evidence for ”