Structural Bioinformatics
Dr. Avraham Samson
Course no.: 81-871
Credit points: 1.5
Final grade is based on 10 assignments
Course homepage: http://odem.md.biu.ac.il/sb871
Bioinformatics
Etymology:
- Bio- from “biology”, and –informatics from
“information science”.
Definition:
– “The collection, archiving, organization, and
interpretation of biological data.” [Orengo, 2003]
2
Bioinformatics
Sequence bioinformatics
Systems biology
Structure bioinformatics
3
4
Structural Bioinformatics
• Focus on data sets with molecular structure
5
Structural Bioinformatics
Motivation 1:
• Detailed
understanding
of molecular
interactions
6
Structural Bioinformatics
Motivation 2:
• Lots of structural data is becoming available
7
Outline of today’s lecture
Overview of structural bioinformatics
– Goals
– Challenges
– Applications
Overview of course
– Topics
– Lectures
– Assignments
8
Structural Bioinformatics
Goals:
• Analysis
• Visualization
• Comparison
• Prediction
• Design
9
Structural Bioinformatics
Goals:
• Analysis
• Visualization
• Comparison
• Prediction
• Design
10
Structural Bioinformatics
Goals:
• Analysis
• Visualization
• Comparison
• Prediction
• Design
11
Structural Bioinformatics
Goals:
• Analysis
• Visualization
• Comparison
• Prediction
• Design
12
Structural Bioinformatics
Goals:
• Analysis
• Visualization
• Comparison
• Prediction
• Design
13
Structural Bioinformatics
Goals:
• Analysis
• Visualization
• Comparison
• Prediction
• Design
14
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
15
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
16
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
17
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
18
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
19
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
20
Structural Bioinformatics
Research challenges:
• Structure prediction
• Binding site detection
• Binding site modeling
• Binding site matching
• Binding prediction
• Molecular design
• etc.
21
Structural Bioinformatics
Applications:
• Biology
• Medicine
• Agriculture
• Industry
• etc.
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Overview of course
http://odem.md.biu.ac.il/sb871
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The Shock of Two Cultures
y = f(x)
 Biologists like experiments, specifics and classifications
They like it better to know many (xi,yi) – 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
(xi,yi)
 One challenge of Computational Biology is to fuse these
two cultures
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