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High-Performance Computational Solutions in Protein Bioinformatics

  • Book
  • © 2014

Overview

Authors:
  1. Dariusz Mrozek

    1. Institue of Informatics, Silesian University of Technology, Gliwice, Poland

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  • Highlights the potential of new computational technologies in protein bioinformatics
  • Presents a focus on protein structure, which remains poorly understood and is not effectively used in medicine
  • Describes methods for applying structural bioinformatics in medical diagnostics
  • Includes supplementary material: sn.pub/extras

Part of the book series: SpringerBriefs in Computer Science (BRIEFSCOMPUTER)

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Table of contents (5 chapters)

  1. Front Matter

    Pages i-xix
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  2. Formal Model of 3D Protein Structures for Functional Genomics, Comparative Bioinformatics, and Molecular Modeling

    • Dariusz Mrozek
    Pages 1-23

  3. Multithreaded PSS-SQL for Searching Databases of Secondary Structures

    • Dariusz Mrozek
    Pages 25-47

  4. Parallel CUDA-Based Protein 3D Structure Similarity Searching

    • Dariusz Mrozek
    Pages 49-79

  5. Cloud Computing for 3D Protein Structure Alignment

    • Dariusz Mrozek
    Pages 81-102

  6. General Discussion and Concluding Remarks

    • Dariusz Mrozek
    Pages 103-106

  7. Back Matter

    Pages 107-109
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Keywords

About this book

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.

Authors and Affiliations

  • Institue of Informatics, Silesian University of Technology, Gliwice, Poland

    Dariusz Mrozek

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