bioinformatics
DESCRIPTION
Introduction to BioinformaticsTRANSCRIPT
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BioinformaticsBioengineering Summer Camp
June 2001Yaron Turpaz, Andrew Binkowski, Jie Liang
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• Introduction
– Basic molecular biology.
• What is Bioinformatics
• UIC’s Bioinformatics group
– Research projects
– Summer camp research project.
Outline
http://gila.engr.uic.edu/bioinformatics/
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DNA
Protein
Nucleotides sequence
Gene expression = Protein production
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Exons & Introns
STOP F R L
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Biological Diversity
Bacteria
Fruit Fly
Human
Yeast
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The Genetic Code• From DNA sequence to Protein sequence.
• 20 Building blocks of a protein = 20 Amino acids.
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From protein sequence to Structure
APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH
=
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Bioinformatics
http://gila.engr.uic.edu/bioinformatics/
• Computational analysis of high-throughput biological data – Whole genome sequencing.– Global genomic expression & profiling.– Functional genomics.– Structural genomics/proteomics– Comparative genomics.
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Bioinformatics in BioE
http://gila.engr.uic.edu/bioinformatics/
• Interdisciplinary approach– Computer science, Mathematics & Statistics.– Molecular biology, Biochemistry & Medicine.
• Rapid growing impact area of BioE:– Boston U, UCBerkeley, UCSD, Rice, WashU, MIT,..
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Research
• Structural genomics/proteomics– Structural basis of functional motifs in protein families.– The CAST server - http://cast.engr.uic.edu/
– Drug discovery.
• Functional genomics– Collaboration with TIGR - http://www.tigr.org/
• Data mining of microbial DNA sequences for detection of foreign DNA.
• Whole genome comparative studies.
• Gene expression analysis– Collaboration with cancer biologist (Dr. Westbrook, School of Medicine)
• Molecular based informatics method to facilitate diagnosis of cancer.
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Gene expressionGene expression
Computational analysis of cDNA microarray expression profiles
~26,000 genes in one experiment
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Functional correlation in clusters
1. Cell division
2. cell signaling/cell communication
3. cell structure/motility
4. cell/organism defense
5. gene/protein expression
6. metabolism
7. unclassified
•Genes with similar expression patterns may participate in the same pathway or may be co-regulated.
•Clustering of expression patterns may reveal such relationships.
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Research – structure & function
How Proteins Interfaces with Other Molecules
• Analysis of protein topographic surfaces: – Identify protein function.– Predicting binding specificity and affinity.– Discovery of functional similarity.
• Protein interaction with cosolvents
– Stabilization of protein solution for longer
shelf life.– Molecular mechanism and optimization.
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Structural genomics/proteomics
• Atlas of Topographic Surfaces of All Known Protein Structures – Automatic identification of binding pockets.– Measurement size of surface binding pockets.
• Drug Discovery– Quantifying ligand accessibility. – Constructing precise negative imprint or cast of binding site.
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Geometry based approach for functional motifs
Discrete FlowDiscrete Flow
Voronoi Diagram and Delaunay TriangulationVoronoi Diagram and Delaunay Triangulation
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3D alpha shapes (HIV-1 protease)
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What is an algorithm?
• Precisely defined procedure for accomplishing a task.– driving directions,
– furniture assembly instructions,
– computer programs.• Built in hardware: fast• Built in software
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Are computers fast enough?
• NP-complete problems:eg. Traveling salesman problem:
20 cities a few seconds
30 cities a few hours
60 cities a few decades
• Computer speed does not increase exponentially.
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Pockets in Ribonuclease APockets in Ribonuclease A
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A Server for Identification of Protein Pockets & Cavities
CASTp
http://cast.engr.uic.edu/
Users of CASTp:Columbia, Harvard, Mayo Clinic, Princeton, Stanford, U Penn, SUNY Stony Brook, Texas A&M, UCIrvine, UBC, Virginia Tech, Yale, Abbott Lab, Pfizer, SmithKline Beecham, ...Agouron, Emisphere, Vertex, ...Kyoto U, Cambridge, European Molecular Biology Lab, INRA (France), Pasteur-Lille, Uppsala, Weizman,...Brazil, Czech, Korea, Turkey, ...
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CASTp ResultsCASTp Results
Calculations:
• Identifies all pockets and cavities.
• Measures the volume and area analytically.
• The number, area, and circumcircles of the mouth openings for each pocket.
Files via email:
• pocket and mouth information file,
• Pocket and mouth atoms,
• a script file for visualization using rasmol.
http://cast.engr.uic.edu/
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THANK YOU