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Creators/Authors contains: "Ayoub, Ron"

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  1. ; (, Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on)
    We have developed 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. Along the way, we introduce a new torsion angle plot without breaks in continuity while still maintaining traditional torsion angle ranges, to assist in identifying separable regions of torsion angles. Subsequently, we introduce a new heuristic we call run position encoding, for handling the lack of specificity of items within character sequences containing runs of repeats. Comparing our results to the output of the CATH structural scan, response times are measured in seconds as opposed to minutes and average RMSDs and TM-scores are better. Our approach is a step towards a comprehensive indexing of protein structures scalable to millions of entries. Code and data are available at https://github.com/rayoub/rupee. 
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