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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
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


recent technical advances
Recent technical advances

Sensitive sequence searches: profiles and HMMs

Large scale computing in cluster environment

Successful design of novel folds and new


example of recent advances 1 genome wide survey

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
examples of recent advances 2 function prediction

Using multiple sequence correlation analysis to characterize functionally important protein regions.

Saraf et al., Protein Eng 2003


Examples of recent advances: 2Function prediction
examples of recent advances 3 protein protein interactions

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 4 targets for structural genomics
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 5 large scale modelling
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.
examples of recent advances 6 docking and inhibitor design

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 7 design of new function
Examples of recent advances: 7Design of new function
  • Computational design of a biologically active enzyme. Dwyer et al., Science 2004, 304:1967-71.

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?



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