Software

Code and data for RUPEE are available at https://github.com/rayoub/rupee

This website and the RUPEE backend make use of the following freely available software.

BioJava

Parsing and aligning protein structures

jQuery

JavaScript library

Bootstrap

HTML styling

PostgreSQL

Backend database

ChemDoodle

3d alignments

References

Please use the second reference for citations.

Initial conference publication.

Ayoub R, Lee Y. RUPEE: Scalable protein structure search using run position encoded residue descriptors. In: 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2017. p. 74–78

Improved and extended.

[CITE] Ayoub R, Lee Y. RUPEE: A fast and accurate purely geometric protein structure search. PLoS ONE. 2019;14(3):1–17

Applied to protein structure prediction.

[or CITE] Ayoub R, Lee Y. Protein structure search to support the development of protein structure prediction methods. Proteins: Structure, Function, and Bioinformatics. 2021;89(6):648-658

For further information, email me at ronaldayoub@gmail.com.