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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


Structural bioinformatics

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: 4 structural biology. Aloy and Russell, targets 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: 5 structural biology. Aloy and Russell, large 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: 7 inhibitor by high-throughput docking. Design of new function

  • Computational design of a biologically active enzyme. Dwyer et al., Science 2004, 304:1967-71.


Structural bioinformatics

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


Structural bioinformatics

Protein folding accuracy. Kuhlman et al., |||

Sequence alignment|||

Protein structure prediction|||||||

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

Side chain prediction||

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


Structural bioinformatics

Protein-protein interactions accuracy. Kuhlman et al., ||||||||||||

Protein-RNA interactions ||

Protein structure analysis|||||

Function prediction |||||

Homology modelling|||

Visualisation server |||

Miscellaneous |||||


Structural bioinformatics

Prediction and Structural Bioinformatics accuracy. Kuhlman et al.,

How does a protein fold?

YNRLCIKPRDWIDECDSNEGGERAYFRNG

KGGCDSFWICPEDHTGADYYSSYRDCFNACI

Papers in this session


Structural bioinformatics

Prediction and Structural Bioinformatics accuracy. Kuhlman et al.,

Can functionally important residues

be recognised?

Can structure prediction lead

to function prediction?


Structural bioinformatics

Prediction and Structural Bioinformatics accuracy. Kuhlman et al.,

How does a protein recognise its ligand?

Paper in this session

What happens subsequent

to ligand binding?


Structural bioinformatics

Prediction and Structural Bioinformatics accuracy. Kuhlman et al.,

How do protein-protein interactions happen?

Paper in this session