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Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints

Published: 11 August 2013 Publication History

Abstract

Analyzing functional interactions between small compounds and proteins is indispensable in genomic drug discovery. Since rich information on various compound-protein inter- actions is available in recent molecular databases, strong demands for making best use of such databases require to in- vent powerful methods to help us find new functional compound-protein pairs on a large scale. We present the succinct interval-splitting tree algorithm (SITA) that efficiently per- forms similarity search in databases for compound-protein pairs with respect to both binary fingerprints and real-valued properties. SITA achieves both time and space efficiency by developing the data structure called interval-splitting trees, which enables to efficiently prune the useless portions of search space, and by incorporating the ideas behind wavelet tree, a succinct data structure to compactly represent trees. We experimentally test SITA on the ability to retrieve similar compound-protein pairs/substrate-product pairs for a query from large databases with over 200 million compound- protein pairs/substrate-product pairs and show that SITA performs better than other possible approaches.

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  • (2017)Scalable Similarity Search for Molecular DescriptorsSimilarity Search and Applications10.1007/978-3-319-68474-1_14(207-219)Online publication date: 28-Sep-2017

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  1. Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints

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      cover image ACM Conferences
      KDD '13: Proceedings of the 19th ACM SIGKDD international conference on Knowledge discovery and data mining
      August 2013
      1534 pages
      ISBN:9781450321747
      DOI:10.1145/2487575
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      Published: 11 August 2013

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      Author Tags

      1. similarity search
      2. succinct data structure
      3. wavelet tree

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      • (2017)Scalable Similarity Search for Molecular DescriptorsSimilarity Search and Applications10.1007/978-3-319-68474-1_14(207-219)Online publication date: 28-Sep-2017

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