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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

slide2

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
Recent technical advances

Sensitive sequence searches: profiles and HMMs

Large scale computing in cluster environment

Successful design of novel folds and new

functions

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

16:397-406.

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.
slide12

Protein folding|||

Sequence alignment|||

Protein structure prediction|||||||

Secondary structure prediction||||||||||

Side chain prediction||

Protein structure comparisons ||||||||||

slide13

Protein-protein interactions||||||||||||

Protein-RNA interactions ||

Protein structure analysis|||||

Function prediction |||||

Homology modelling|||

Visualisation server |||

Miscellaneous |||||

slide14

Prediction and Structural Bioinformatics

How does a protein fold?

YNRLCIKPRDWIDECDSNEGGERAYFRNG

KGGCDSFWICPEDHTGADYYSSYRDCFNACI

Papers in this session

slide15

Prediction and Structural Bioinformatics

Can functionally important residues

be recognised?

Can structure prediction lead

to function prediction?

slide16

Prediction and Structural Bioinformatics

How does a protein recognise its ligand?

Paper in this session

What happens subsequent

to ligand binding?

slide17

Prediction and Structural Bioinformatics

How do protein-protein interactions happen?

Paper in this session

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