![](/images/graphics-bg.png)
Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection
Joint Authors
Chapuis, Guillaume
Le Boudic-Jamin, Mathilde
Andonov, Rumen
Djidjev, Hristo
Lavenier, Dominique
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-03-31
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
Finding similarities between protein structures is a crucial task in molecular biology.
Most of the existing toolsrequire proteins to be aligned in order-preserving way and only find single alignments even when multiple similar regions exist.
We propose a new seed-based approach that discovers multiple pairs of similar regions.
Its computational complexity is polynomialand it comes with a quality guarantee—the returned alignments have both root mean squared deviations (coordinate-based as well as internal-distances based) lower than a given threshold, if such exist.
We do not require the alignments to be order preserving (i.e., we consider nonsequential alignments), which makes our algorithm suitable for detecting similar domains when comparing multidomain proteins as well as to detect structural repetitions within a single protein.
Because the search space for nonsequential alignments is much larger than for sequential ones, the computational burden is addressed by extensive use of parallelcomputing techniques: a coarse-grain level parallelism making use of available CPU cores for computation and a fine-grain level parallelism exploiting bit-level concurrency as well as vector instructions.
American Psychological Association (APA)
Chapuis, Guillaume& Le Boudic-Jamin, Mathilde& Andonov, Rumen& Djidjev, Hristo& Lavenier, Dominique. 2015. Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection. Scientific Programming،Vol. 2015, no. 2015, pp.1-12.
https://search.emarefa.net/detail/BIM-1076510
Modern Language Association (MLA)
Chapuis, Guillaume…[et al.]. Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection. Scientific Programming No. 2015 (2015), pp.1-12.
https://search.emarefa.net/detail/BIM-1076510
American Medical Association (AMA)
Chapuis, Guillaume& Le Boudic-Jamin, Mathilde& Andonov, Rumen& Djidjev, Hristo& Lavenier, Dominique. Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection. Scientific Programming. 2015. Vol. 2015, no. 2015, pp.1-12.
https://search.emarefa.net/detail/BIM-1076510
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1076510