Structural Bioinformatics

underlingbuddhaBiotechnology

Oct 2, 2013 (4 years and 10 days ago)

92 views

Structural Bioinformatics

Dr. Avraham Samson

Course no.: 81
-
871

Credit points: 1.5

Final grade is based on 10 projects

Course homepage: ari.stanford.edu/sb871



2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

2

Course homepage:
http://ari.stanford.edu/sb871


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

3

Outline


Overview of structural bioinformatics


Goals


Challenges


Applications


Overview of course


Goals


Lectures


Coursework


Projects

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

4

Bioinformatics

Definition:


“The collection, archiving, organization, and
interpretation of biological data.” [Orengo,
2003]

Generally speaking:


Large biological data sets


Computer representations and algorithms


Storage, analysis, visualization, prediction,
and design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

5

Bioinformatics

Etymology:


Bio
-

from “biology”, and

informatics from “information
science”.


Structural bioinformatics

-
Structure determination

-
Structure prediction

-
Binding site prediction

-
Interactions

-
Molecular dynamics

Sequence bioinformatics

-
Pair
-
wise sequence alignment

-
Multiple sequence alignment

-
Hidden Markov model

-
Phylogenetic analysis

-
Evolution clocks

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

6

Structural Bioinformatics


Focus on data sets with molecular
structure

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

7

Structural Bioinformatics

Motivation 1:


Detailed
understanding
of molecular
interactions

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

8

Structural Bioinformatics


Motivation 2:


Lots of
structural
data is
becoming
available

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

9

Structural Bioinformatics

Goals:



Analysis

• Visualization

• Comparison

• Prediction

• Design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

10

Structural Bioinformatics

Goals:

• Analysis

• Visualization

• Comparison

• Prediction

• Design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

11

Structural Bioinformatics

Goals:



Analysis


Visualization

• Comparison

• Prediction

• Design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

12

Structural Bioinformatics

Goals:



Analysis

• Visualization


Comparison

• Prediction

• Design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

13

Structural Bioinformatics

Goals:



Analysis

• Visualization

• Comparison


Prediction

• Design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

14

Structural Bioinformatics

Goals:



Analysis

• Visualization

• Comparison

• Prediction

• Design


2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

15

Structural Bioinformatics

Research challenges:

• Structure prediction

• Binding site detection

• Binding site modeling

• Binding site matching

• Binding prediction

• Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

16

Structural Bioinformatics

Research challenges:

• Structure prediction

• Binding site detection

• Binding site modeling

• Binding site matching

• Binding prediction

• Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

17

Structural Bioinformatics

Research challenges:

• Structure prediction


Binding site detection

• Binding site modeling

• Binding site matching

• Binding prediction

• Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

18

Structural Bioinformatics

Research challenges:

• Structure prediction

• Binding site detection


Binding site modeling

• Binding site matching

• Binding prediction

• Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

19

Structural Bioinformatics

Research challenges:

• Structure prediction

• Binding site detection

• Binding site modeling


Binding site matching

• Binding prediction

• Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

20

Structural Bioinformatics

Research challenges:

• Structure prediction

• Binding site detection

• Binding site modeling

• Binding site matching


Binding prediction

• Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

21

Structural Bioinformatics

Research challenges:

• Structure prediction

• Binding site detection

• Binding site modeling

• Binding site matching

• Binding prediction


Molecular design

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

22

Structural Bioinformatics

Applications:

• Biology

• Medicine

• Agriculture

• Industry

• etc.

2012

Avraham Samson
-

Faculty of
Medicine
-

Bar Ilan University

23

y = f(x)



Biologists

like experiments, specifics and classifications


They like it better to know many
(x
i
,y
i
)



i.e., facts


and
classify them, than to know
f



Computer scientists like simulation, abstractions, and
general algorithms




They want to know
f



the explanation of the facts


and
efficient ways to compute it, but rarely care for any
(x
i
,y
i
)



One challenge of Computational Biology is to fuse these
two cultures

The Shock of Two Cultures