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High-Performance Computational Solutions in Protein Bioinformatics [electronic resource] / by Dariusz Mrozek.

By: Mrozek, Dariusz [author.].
Contributor(s): SpringerLink (Online service).
Material type: materialTypeLabelBookSeries: SpringerBriefs in Computer Science: Publisher: Cham : Springer International Publishing : Imprint: Springer, 2014Description: XIX, 109 p. 56 illus., 21 illus. in color. online resource.Content type: text Media type: computer Carrier type: online resourceISBN: 9783319069715.Subject(s): Computer science | Microprocessors | Computer communication systems | Bioinformatics | Proteins | Biomathematics | Computer Science | Computational Biology/Bioinformatics | Computer Communication Networks | Protein Structure | Bioinformatics | Processor Architectures | Mathematical and Computational BiologyAdditional physical formats: Printed edition:: No titleDDC classification: 570.285 Online resources: Click here to access online
Contents:
Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling -- Multithreaded PSS-SQL for Searching Databases of Secondary Structures -- GPU and CUDA for 3D Protein Structure Similarity Searching -- Cloud Computing for 3D Protein Structure Alignment -- General Discussion and Concluding Remarks.
In: Springer eBooksSummary: Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels, and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics, and molecular modeling. The second part focuses on the use of multithreading for efficient approximate searching on protein secondary structures. The third and fourth parts concentrate on finding 3D protein structure similarities with the support of GPUs and cloud computing. Parts three and four both describe the acceleration of different methods. The text will be of interest to researchers and software developers working in the field of structural bioinformatics and biomedical databases.
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Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling -- Multithreaded PSS-SQL for Searching Databases of Secondary Structures -- GPU and CUDA for 3D Protein Structure Similarity Searching -- Cloud Computing for 3D Protein Structure Alignment -- General Discussion and Concluding Remarks.

Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels, and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics, and molecular modeling. The second part focuses on the use of multithreading for efficient approximate searching on protein secondary structures. The third and fourth parts concentrate on finding 3D protein structure similarities with the support of GPUs and cloud computing. Parts three and four both describe the acceleration of different methods. The text will be of interest to researchers and software developers working in the field of structural bioinformatics and biomedical databases.

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