Protein Bioinformatics

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

Michael is a frequent invited speaker to local conferences and universities in India and to

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.

A protein structure oriented bioinformatics book has been long overdue and I would like to congratulate Dr. Gromiha for his efforts to fill this gap. Dr. Sandeep Kumar, Principle Scientist, Pharmaceutical Sciences, Research and Development, Global Biologics, Pfizer, Inc. The book has excellent coverage for students wishing to practise bioinformatics Dr. Debnath Pal, Assistant Professor, IISC Bangalore

A protein structure oriented bioinformatics book has been long overdue and I would like to congratulate Dr. Gromiha for his efforts to fill this gap. Dr. Sandeep Kumar, Principle Scientist, Pharmaceutical Sciences, Research and Development, Global Biologics, Pfizer, Inc.

The book has excellent coverage for students wishing to practise bioinformatics Dr. Debnath Pal, Assistant Professor, IISC Bangalore