Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors

DOI10.3390/A2020692MaRDI QIDQ1662475zbMATH OpenOpenAlexFDO

Authors Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner

Publication date 20 August 2018

Published in Algorithms (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3390/a2020692

zbMATH Keywords

RNAtorsion anglesproteinhash tablestructural alignmentn-gram

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30)

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Cites work

• Algorithms on Strings, Trees and Sequences
• Dynamic Perfect Hashing: Upper and Lower Bounds
• Introduction to algorithms
• PSIST: a scalable approach to indexing protein structures using suffix trees

Cited in

(3)

• PSIST: a scalable approach to indexing protein structures using suffix trees
• A novel algorithm for macromolecular epitope matching
• 3D-hit: fast structural comparison of proteins on multicore architectures

Describes a project that uses

Uses Software

• SCOPmap
• TM-align
• SARSA
• BioJava

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