Structural Bioinformatics - National Centre for Biological Sciences

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2 Οκτ 2013 (πριν από 4 χρόνια και 1 μήνα)

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Structural Bioinformatics

R. Sowdhamini


National Centre for Biological Sciences


Tata Institute of Fundamental Research

Bangalore, INDIA

1. Prediction of Secondary Structure and

Tertiary Interactions in Proteins

How to predict

-
sheets?

Problems in prediction:

-

Sequentially distant


interactions;

-

Non
-
ideal nature

Relevance: protein

structure prediction

Picture taken from Branden & Tooze book

Three
-
Stage Prediction of Protein
Beta
-
Sheets by Neural Networks,
Alignments, and Graph
Algorithms




Authors:

Cheng,
Baldi

Paper in this session

2.

Ab
-
initio

prediction of protein structure

How does a protein fold?

YNRLCIKPRDWIDECDSNEGGERAYFRNG

KGGCDSFWICPEDHTGADYYSSYRDCFNACI

Picture taken from Branden & Tooze book

Improving Protein Structure
Prediction With Model
-
Based
Search




Authors:
Brunette, Brock


Paper in this session

3. Prediction of active sites of proteins

Can active site residues be recognised?

Relevance in Structural

Genomics initiative

Problems:

too many

cavities in structures!

Limitations:

paucity

of sequence homologues

Picture taken from Sowdhamini’s lab

Prediction of Active Sites for
Protein Structures from
Computed Chemical Properties




Authors:
Ko, Murga,
Ondrechen


Paper in this session

4. Prediction of functionally important

regions in proteins

Can functionally important residues

be recognised?

Can structure prediction lead

to function prediction?

Picture taken from Sowdhamini’s lab

In silico

Identification of
Functional Regions in Proteins




Authors:
Nimrod, Glaser,
Steinberg, Ben
-
Tal, Pupko

Paper in this session

5. Objective measurement of evolutionary

timescales of protein folds

Can the age of a protein fold be determined?

Relevance to protein

Fold evolution

Limitations:

accurate

Descriptor of age of fold;

Limited number of data

Picture taken from Mark Gernstein’s Lab Web page

How Old is Your Fold?




Authors:

Winstanley,
Abeln, Deane


Paper in this session

6. Prediction of folding nuclei in proteins

Can residues that initiate folding in a protein

be recognised?

Relevance: biophysics of

Protein unfolding/folding events

Limitations:

absence of

accurate energy functions;

Dependence on availability

df sequence homologues

Picture taken from Jayant Udgaonkar’s Lab Web page

Search for Folding Nuclei in
Native Protein Structures




Authors:

Shmygelska


Paper in this session

7. Prediction of conformational changes

in proteins

How to simulate changes in flexible parts

of proteins?

Limitations:

accurate

Description of energy

Functions;

Macromolecular

nature

Relevance to biological processes

Picture taken from Mark Gernstein’s Lab Web page

A Path Planning Approach for
Computing Large
-
Amplitude
Motions of Flexible Molecules




Authors:
Cortes, Simeon, Ruiz de
Angulo, Guieysse, Remaud
-
Simeon, Tran


Paper in this session