Sternbergx - Edmond J. Safra Bioinformatics Program

richessewoozyBiotechnology

Oct 1, 2013 (3 years and 9 months ago)

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You are cordially invited to a talk of the Edmond J. Safra Center for
Bioinformatics Distinguished Speaker Series
.

The speaker is Prof. Michael
Sternberg, Director CISBIO, Centre for
Integrative Systems Biology and Bioinformatics, Imperial College London,

www.imperial.ac.uk/cisbio
.


Title:
Modelling Protein Structure, Function and Networks


Time
:
Sunday, 18 March 2012, at 12:15 (refreshments from 12:00)




Place
:


Orenstein 103
,
School of Chemistry,


Exact
Sciences Faculty


Abstract:
This talk will present a summary of protein modelling software developed in my
group all of which is available from our web site.

Poing
is a program which uses a simplified
representation of the protein (2 centres per residue) and simplified interactions to simulate
the folding of a protein.


We have used it to explore folding in the crowded environment of
the cell.


Poing

has also been ad
ded into
Phyre2

which performs protein fold recognition
using a known template to provide the basis for the prediction.


Phyre2

is widely used by the
community with over 2,000 runs /week from the community.Several tools have been
developed for protein func
tion prediction.
ConFunc
predicts gene ontology (GO) terms from
a sequence based on deriving sequence profiles supervised by GO terms of homologues.


Recently
ConFunc

has been incorporated


with other function prediction to tools in
CombFunc
.


A related pr
oblem of identifying ligand binding sites in a protein structure has
the subject addressed by
3DLigandSite
. With the elucidation of protein
-
protein interaction
network, tools are required to extract comparative information from these data.


We have
develop
ed
PINALOG

to perform a global alignment of two interactomes.


The scoring
function combines sequence homology, functional similarity, and correspondence of the
local network graph.


PINALOG

provides a valuable resource for extrapolating from one
species t
o another for protein function prediction and to identify protein complexes. Poing


Jefferys, B. R., Kelley, L. A. & Sternberg, M. J. (2010). Protein folding requires crowd control
in a simulated cell.

Journal of molecular biology

397, 1329
-
38. Phyre
-

Ke
lley, L. A. &
Sternberg, M. J. (2009). Protein structure prediction on the Web: a case study using the
Phyre server.

Nature protocols

4, 363
-
71. ConFunc


-

Wass, M. N. & Sternberg, M. J. (2008).
ConFunc
--
functional annotation in the twilight zone.

Bioinfor
matics

24, 798
-
806. 3DLigand
Site
-

Wass, M. N., Kelley, L. A. & Sternberg, M. J. (2010). 3DLigandSite: predicting ligand
-
binding sites using similar structures.

Nucleic acids research

38, W469
-
73. CombFunc


Wass
& Sternberg under review PINALOG


Phan, H

& Sternberg, M.J.E. PINALOG: a novel
approach to align protein interaction networks
-

implications for complex detection and
function prediction. Bioinformatics in the press.


Host: Prof. Haim Wolfson, (x5373
,
haim.wolfson@gmail.com
), School of
Computer Science, Tel Aviv University.

If you would like to meet with him, please send an e
-
mail to Haim Wolfson.