Advances in Structural Bioinformatics: Prediction, Folding, Function, and Interaction, Slides of Biochemistry

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Structural Bioinformatics

Prediction with inputs from Structural Bioinformatics

Genome-wide analysis of protein families

Evolutionary relationships amongst proteins

Design of new function to an existing scaffold

Design of novel protein folds

Example of recent advances: 1

Genome-wide survey

• Mechanisms of thermal adaptation revealed from the genome of the antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Saunders et al., Genome Res 2003 (7):1580-

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: 4

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

• 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: 7

Design of new function

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

Examples of recent advances: 8

Design of novel fold

• Design of a novel globular protein fold with

atomic-level accuracy. Kuhlman et al., Science 2003, 302:1364-8.

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

YNRLCIKPRDWIDECDSNEGGERAYFRNG KGGCDSFWICPEDHTGADYYSSYRDCFNACI

Prediction and Structural Bioinformatics

What happens subsequent to ligand binding?

Paper in this session

How does a protein recognise its ligand?

Prediction and Structural Bioinformatics

How do protein-protein interactions happen?

Paper in this session