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Structural Bioinformatics. R. Sowdhamini National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore, INDIA. Prediction with inputs from Structural Bioinformatics. Genome-wide analysis of protein families. Evolutionary relationships amongst proteins.
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Structural Bioinformatics R. Sowdhamini National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore, INDIA
Prediction with inputs from Structural Bioinformatics Genome-wide analysis of protein families Evolutionary relationships amongst proteins Design of novel protein folds Design of new function to an existing scaffold
Recent technical advances Sensitive sequence searches: profiles and HMMs Large scale computing in cluster environment Successful design of novel folds and new functions
Mechanisms of thermal adaptationrevealed from the genome of the antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Saunders et al., Genome Res 2003 (7):1580-8 Example of recent advances: 1Genome-wide survey
Using multiple sequence correlation analysis to characterize functionally important protein regions. Saraf et al., Protein Eng 2003 16:397-406. Examples of recent advances: 2Function prediction
Interrogating protein interaction networks through structural biology. Aloy and Russell, Proc Natl Acad Sci U S A. 2002, 99:5896-901. Examples of recent advances: 3Protein-protein interactions
Examples of recent advances: 4targets for structural genomics • Automatic target selection for structural genomics on eukaryotes. • Liu et al., Proteins, 2004, 56:188-200.
Examples of recent advances: 5large scale modelling • Protein structure prediction for the male-specific region of the human Y chromosome. Ginalski et al., Proc Natl Acad Sci U S A. 2004, 101:2305-10. • Comparative protein structure modeling by iterative alignment, model building and model assessment. John & Sali Nucleic Acids Res. 2003, 31:3982-92.
Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. Vangrevelinghe et al.,J Med Chem. 2003, 46:2656-62. Structural modes of stabilization of permissive phosphorylation sites in protein kinases: distinct strategies in Ser/Thr and Tyr kinases. Krupa et al., J Mol Biol. 2004, 339:1025-39. Examples of recent advances: 6Docking and inhibitor design
Examples of recent advances: 7Design of new function • Computational design of a biologically active enzyme. Dwyer et al., Science 2004, 304:1967-71.
Design of a novel globular protein fold with atomic-level accuracy. Kuhlman et al., Science 2003, 302:1364-8. Examples of recent advances: 8Design of novel fold
Protein folding||| Sequence alignment||| Protein structure prediction||||||| Secondary structure prediction|||||||||| Side chain prediction|| Protein structure comparisons ||||||||||
Protein-protein interactions|||||||||||| Protein-RNA interactions || Protein structure analysis||||| Function prediction ||||| Homology modelling||| Visualisation server ||| Miscellaneous |||||
Prediction and Structural Bioinformatics How does a protein fold? YNRLCIKPRDWIDECDSNEGGERAYFRNG KGGCDSFWICPEDHTGADYYSSYRDCFNACI Papers in this session
Prediction and Structural Bioinformatics Can functionally important residues be recognised? Can structure prediction lead to function prediction?
Prediction and Structural Bioinformatics How does a protein recognise its ligand? Paper in this session What happens subsequent to ligand binding?
Prediction and Structural Bioinformatics How do protein-protein interactions happen? Paper in this session
