High-Performance Computational Solutions in Protein Bioinformatics

1. Front Matter

   Pages i-xix

   PDF

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

   PDF

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.

• Amino Acid Sequence
• Bioinformatics
• Cloud Computing
• GPU, CUDA
• Multi-Agent Systems
• Multithreaded Processing
• Parallel Processing
• Protein Structure
• Proteins

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

  Dariusz Mrozek

Policies and ethics