High-Performance Computational Solutions in Protein Bioinformatics

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.

List of 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.

Product details

• Authors: Dariusz Mrozek
• Publisher: Springer, Berlin
• Languages: English
• Product format: Paperback / Softback
• Released: 01.07.2014
• EAN: 9783319069708
• ISBN: 978-3-31-906970-8
• No. of pages: 109
• Dimensions: 156 mm x 239 mm x 7 mm
• Weight: 237 g
• Illustrations: XIX, 109 p. 56 illus., 21 illus. in color.
• Series: SpringerBriefs in Computer Science
• Subjects: Natural sciences, medicine, IT, technology > Biology > Miscellaneous; C, Microprocessors, computer science, biochemistry, molecular biology, bioinformatics, proteins, Computer Communication Networks, Information technology: general issues, Maths for scientists, Computational and Systems Biology, Computational Biology/Bioinformatics, Biomathematics, Mathematical and Computational Biology, Computer architecture & logic design, Processor Architectures, Computer communication systems, Network hardware, Protein Structure