Protein Bioinformatics
From Sequence to Function
Description
Key Features
- Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions
- Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.
Readership
Undergraduate and post graduate students enrolled in courses on bioinformatics, protein bioinformatics, proteomics, protein engineering, structural bioinformatics, computational biology.
Researchers in proteomics, bioinformatics, biophysics, computational biology, molecular modeling, and drug design
Table of Contents
1 Proteins
1.1 Building blocks
1.2 Hierarchical representation of proteins
1.3 Structural classification of proteins
1.4 Databases for protein sequences
1.5 Exercises
1.6 References
2. Protein Sequence Analysis
2.1 Sequence alignment
2.2 Programs for aligning protein sequences
2.3 Amino acid properties
2.4 Amphipathic character of a-helices and b-strands
2.5 Online tools for sequence analysis
2.6 Exercises
2.7 References
3 Protein Structure Analysis
3.1 Assignment of secondary structures
3.2 Computation of solvent accessibility
3.3 Representation of solvent accessibility
3.4 Residue-residue contacts
3.5 Amino acid clusters in protein structures
3.6 Contact potentials
3.7 Cation--p interactions in protein structures
3.8 Non canonical interactions
3.9 Free energy calculations
3.10 Amino acid properties derived from protein structural data
3.11 Parameters for proteins
3.12 Exercises
3.13 References
4. Protein Folding Kinetics
4.1 F value analysis
4.2 Experimental studies
4.3 Relationship between amino acid properties and F values
4.4 Hydrophobic clusters and long-range contact network in F value analysis
4.5 Kinetic database for proteins
4.6 Prediction of protein folding rates
4.7 Relationship between F values and folding rates
4.8 References
5. Protein Structure Prediction
5.1 Secondary structure
5.2 Protein structural class
5.3 Secondary structure content
5.4 Discrimination of transmembrane helical proteins and predicting their membrane spanning segments
5.5 Discrimination of transmembrane strand proteins
5.6 Identification of membrane spanning b -strand segments
5.7 Solvent accessibility
5.8 Inter-residue contact prediction
5.9 Protein tertiary structure prediction
5.10 Webservers for protein structure prediction
5.11 Exercises
5.12 References
6 Protein Stability
6.1 Determination of protein stability
6.2 Thermodynamic database for proteins and mutants
6.3 Relative contribution of non-covalent interactions to protein stability
6.4 Stability of thermophilic proteins
6.5 Analysis and Prediction of protein mutant stability
6.6 Exercises
6.7 References
7 Protein Interactions
7.1 Protein-protein interactions
7.2 Protein-DNA interactions
7.3 Protein-RNA interactions
7.4 Protein-ligand interactions
7.5 Exercises
7.6 References
Appendix A List of protein databases/webservers
Product details
- No. of pages: 339
- Language: English
- Copyright: © Academic Press 2010
- Published: August 31, 2010
- Imprint: Academic Press
- eBook ISBN: 9780123884244
- Paperback ISBN: 9788131222973
About the Author
M. Michael Gromiha
international conferences focused on bioinformatics, computational biology and
molecular biology. He maintains close connections with research and teaching
colleagues in India and contributes to international publications including handbooks,
encyclopedias and journals. He began his research on Computational Molecular
Biophysics in 1989, earning the PhD in BioPhysics from Bharathidasan University,
India. He gained his first Post Doctoral experience on DNA bending and protein-DNA
interactions at International Center for Genetic Engineering and Biotechnology (ICGEB),
Italy. He developed databases for proteins and computer simulation of protein-DNA
interactions during his subsequent postdoc at The Institute of Physical and Chemical
Research (RIKEN), Japan. At AIST he continues to focus on various aspects of protein
bioinformatics.