Protein Bioinformatics

Michael is a frequent invited speaker to local conferences and universities in India and tointernational conferences focused on bioinformatics, computational biology andmolecular biology. He maintains close connections with research and teachingcolleagues in India and contributes to international publications including handbooks,encyclopedias and journals. He began his research on Computational MolecularBiophysics in 1989, earning the PhD in BioPhysics from Bharathidasan University,India. He gained his first Post Doctoral experience on DNA bending and protein-DNAinteractions at International Center for Genetic Engineering and Biotechnology (ICGEB),Italy. He developed databases for proteins and computer simulation of protein-DNAinteractions during his subsequent postdoc at The Institute of Physical and ChemicalResearch (RIKEN), Japan. At AIST he continues to focus on various aspects of proteinbioinformatics.

"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

• 1 Proteins1.1 Building blocks1.2 Hierarchical representation of proteins1.3 Structural classification of proteins1.4 Databases for protein sequences1.5 Exercises1.6 References2. Protein Sequence Analysis2.1 Sequence alignment2.2 Programs for aligning protein sequences2.3 Amino acid properties2.4 Amphipathic character of a-helices and b-strands2.5 Online tools for sequence analysis2.6 Exercises2.7 References3 Protein Structure Analysis3.1 Assignment of secondary structures3.2 Computation of solvent accessibility3.3 Representation of solvent accessibility3.4 Residue-residue contacts3.5 Amino acid clusters in protein structures3.6 Contact potentials3.7 Cation--p interactions in protein structures3.8 Non canonical interactions3.9 Free energy calculations3.10 Amino acid properties derived from protein structural data3.11 Parameters for proteins3.12 Exercises3.13 References4. Protein Folding Kinetics4.1 F value analysis4.2 Experimental studies4.3 Relationship between amino acid properties and F values4.4 Hydrophobic clusters and long-range contact network in F value analysis4.5 Kinetic database for proteins4.6 Prediction of protein folding rates4.7 Relationship between F values and folding rates4.8 References5. Protein Structure Prediction5.1 Secondary structure5.2 Protein structural class5.3 Secondary structure content5.4 Discrimination of transmembrane helical proteins and predicting their membrane spanning segments5.5 Discrimination of transmembrane strand proteins5.6 Identification of membrane spanning b -strand segments5.7 Solvent accessibility5.8 Inter-residue contact prediction5.9 Protein tertiary structure prediction5.10 Webservers for protein structure prediction5.11 Exercises5.12 References6 Protein Stability6.1 Determination of protein stability6.2 Thermodynamic database for proteins and mutants6.3 Relative contribution of non-covalent interactions to protein stability6.4 Stability of thermophilic proteins6.5 Analysis and Prediction of protein mutant stability6.6 Exercises6.7 References7 Protein Interactions7.1 Protein-protein interactions7.2 Protein-DNA interactions7.3 Protein-RNA interactions7.4 Protein-ligand interactions7.5 Exercises7.6 ReferencesAppendix A List of protein databases/webservers