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

DOI10.3390/a2020692zbMath1461.92029OpenAlexW2151651919MaRDI QIDQ1662475

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

Publication date: 20 August 2018

Published in: Algorithms (Search for Journal in Brave)

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

zbMATH Keywords

structural alignmentproteinRNAtorsion angleshash tablen-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)

Uses Software

• BioJava
• SARSA
• TM-align
• SCOPmap

Cites Work

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