Bioinformatics

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Introduction to Bioinformatics

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  • Bioinformatics

    1. 1. Bioinformatics <ul><li>Bioengineering Summer Camp </li></ul><ul><li>June 2001 </li></ul><ul><li>Yaron Turpaz, Andrew Binkowski, Jie Liang </li></ul>
    2. 2. <ul><li>Introduction </li></ul><ul><ul><li>Basic molecular biology. </li></ul></ul><ul><li>What is Bioinformatics </li></ul><ul><li>UIC’s Bioinformatics group </li></ul><ul><ul><li>Research projects </li></ul></ul><ul><ul><li>Summer camp research project. </li></ul></ul>Outline http://gila.engr.uic.edu/bioinformatics/
    3. 3. DNA Protein Nucleotides sequence Gene expression = Protein production
    4. 4. Exons & Introns STOP F R L
    5. 5. Biological Diversity Bacteria Fruit Fly Human Yeast
    6. 6. The Genetic Code <ul><li>From DNA sequence to Protein sequence. </li></ul><ul><li>20 Building blocks of a protein = 20 Amino acids. </li></ul>
    7. 7. From protein sequence to Structure <ul><li>APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH </li></ul>=
    8. 8. <ul><li>Computational analysis of high-throughput biological data </li></ul><ul><ul><li>Whole genome sequencing. </li></ul></ul><ul><ul><li>Global genomic expression & profiling. </li></ul></ul><ul><ul><li>Functional genomics. </li></ul></ul><ul><ul><li>Structural genomics/proteomics </li></ul></ul><ul><ul><li>Comparative genomics. </li></ul></ul>Bioinformatics http://gila.engr.uic.edu/bioinformatics/
    9. 9. <ul><li>Interdisciplinary approach </li></ul><ul><ul><li>Computer science, Mathematics & Statistics. </li></ul></ul><ul><ul><li>Molecular biology, Biochemistry & Medicine. </li></ul></ul><ul><li>Rapid growing impact area of BioE: </li></ul><ul><ul><li>Boston U, UCBerkeley, UCSD, Rice, WashU, MIT,.. </li></ul></ul>Bioinformatics in BioE http://gila.engr.uic.edu/bioinformatics/
    10. 10. <ul><li>Structural genomics/proteomics </li></ul><ul><ul><li>Structural basis of functional motifs in protein families. </li></ul></ul><ul><ul><li>The CAST server - http://cast.engr.uic.edu/ </li></ul></ul><ul><ul><li>Drug discovery. </li></ul></ul><ul><li>Functional genomics </li></ul><ul><ul><li>Collaboration with TIGR - http://www.tigr.org/ </li></ul></ul><ul><ul><ul><li>Data mining of microbial DNA sequences for detection of foreign DNA. </li></ul></ul></ul><ul><ul><ul><li>Whole genome comparative studies. </li></ul></ul></ul><ul><li>Gene expression analysis </li></ul><ul><ul><li>Collaboration with cancer biologist (Dr. Westbrook, School of Medicine)‏ </li></ul></ul><ul><ul><ul><li>Molecular based informatics method to facilitate diagnosis of cancer. </li></ul></ul></ul>Research
    11. 11. Gene expression Computational analysis of cDNA microarray expression profiles ~26,000 genes in one experiment
    12. 12. 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 <ul><li>Genes with similar expression patterns may participate in the same pathway or may be co-regulated. </li></ul><ul><li>Clustering of expression patterns may reveal such relationships. </li></ul>
    13. 13. How Proteins Interfaces with Other Molecules <ul><li>Analysis of protein topographic surfaces: </li></ul><ul><ul><li>Identify protein function. </li></ul></ul><ul><ul><li>Predicting binding specificity and affinity. </li></ul></ul><ul><ul><li>Discovery of functional similarity. </li></ul></ul><ul><li>Protein interaction with cosolvents </li></ul><ul><ul><li>Stabilization of protein solution for longer shelf life. </li></ul></ul><ul><ul><li>Molecular mechanism and optimization. </li></ul></ul>Research – structure & function
    14. 14. <ul><li>Atlas of Topographic Surfaces of All Known Protein Structures </li></ul><ul><ul><li>Automatic identification of binding pockets. </li></ul></ul><ul><ul><li>Measurement size of surface binding pockets. </li></ul></ul><ul><li>Drug Discovery </li></ul><ul><ul><li>Quantifying ligand accessibility. </li></ul></ul><ul><ul><li>Constructing precise negative imprint or cast of binding site. </li></ul></ul>Structural genomics/proteomics
    15. 15. Voronoi Diagram and Delaunay Triangulation Geometry based approach for functional motifs Discrete Flow
    16. 16. 3D alpha shapes (HIV-1 protease)‏
    17. 17. What is an algorithm? <ul><li>Precisely defined procedure for accomplishing a task. </li></ul><ul><ul><li>driving directions, </li></ul></ul><ul><ul><li>furniture assembly instructions, </li></ul></ul><ul><ul><li>computer programs. </li></ul></ul><ul><ul><ul><li>Built in hardware: fast </li></ul></ul></ul><ul><ul><ul><li>Built in software </li></ul></ul></ul>
    18. 18. Are computers fast enough? <ul><li>NP-complete problems: </li></ul><ul><ul><ul><li>eg. Traveling salesman problem : </li></ul></ul></ul><ul><ul><ul><li>20 cities a few seconds </li></ul></ul></ul><ul><ul><ul><li>30 cities a few hours </li></ul></ul></ul><ul><ul><ul><li>60 cities a few decades </li></ul></ul></ul><ul><li>Computer speed does not increase exponentially. </li></ul>
    19. 19. Pockets in Ribonuclease A
    20. 20. 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, ...
    21. 21. CASTp Results <ul><li>Calculations: </li></ul><ul><li>Identifies all pockets and cavities.  </li></ul><ul><li>Measures the volume and area analytically.  </li></ul><ul><li>The number, area, and circumcircles of the mouth openings for each pocket.  </li></ul><ul><li>Files via email: </li></ul><ul><li>pocket and mouth information file, </li></ul><ul><li>Pocket and mouth atoms, </li></ul><ul><li>a script file for visualization using rasmol.   </li></ul>http://cast.engr.uic.edu/
    22. 22. THANK YOU

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