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EECS 800 Research Seminar Mining Biological Data

EECS 800 Research Seminar Mining Biological Data. Instructor: Luke Huan Fall, 2006. Lys. Lys. Gly. Gly. Leu. Val. Ala. His. Cartoon. Space filling. Oxygen Nitrogen Carbon Sulfur. Ribbon. Surface. Introduction. Protein A sequence from 20 amino acids

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EECS 800 Research Seminar Mining Biological Data

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  1. EECS 800 Research SeminarMining Biological Data Instructor: Luke Huan Fall, 2006

  2. Lys Lys Gly Gly Leu Val Ala His Cartoon Space filling Oxygen Nitrogen Carbon Sulfur Ribbon Surface Introduction • Protein • A sequence from 20 amino acids • Adopts a stable 3D structure that can be measured experimentally

  3. Growth of Known Structures in Protein Data Bank 35,000 The total number of known protein structures Newly characterized proteins in that year # of structures 1988 2005 Year Exponential Growth of Protein Structures

  4. Protein Structure Space http://www.nigms.nih.gov/psi/

  5. Structure Space is Described Hierarchically • From SCOP: Structure classification of proteins (http://scop.berkeley.edu/) • Class • Fold • Superfamily • Family • Protein domains

  6. SCOP Statistics 25973 PDB Entries (July 2005). 70859 Domains.

  7. Amino Acids: Building Blocks of Proteins

  8. 20 Naturally-occurring Amino Acids

  9. Protein Secondary Structure • α Helix

  10. Protein Secondary Structure • β strands

  11. Top Level of Structure Space: Structure Classes • There are four major classes: • α proteins • β proteins • α + β (anti-parallel β strands) • α / β (parallel β strands).

  12. Protein Folds • Protein fold is the way how secondary structures are organized in a 3D structure.

  13. Popular Folds The eight most frequent SCOP folds

  14. Superfamily and Family • Proteins within the same superfamily and family will tend to have similar sequence and similar function

  15. …. The Nature of Protein Structure Data • The ball-stick model is an element-based structure representation • A structure is decomposed into a set of amino acids • Proteingeometry,topology,andattributesare defined with respect to the amino acid set • Geometry is the coordinates of amino acids • Topology is the phyisco-chemical interactions of the residues • Attributes are the physico-chemical properties of the residues

  16. Part of the biological system in a cell at the molecular level Grant Challenges: Proteomics Source: http://www.ircs.upenn.edu/modeling2001/,

  17. References • Bioinformatics: Genes, Proteins, and Computers, Christine Orengo, David Jones, Janet Thornton edit, Bios Scientific Publishers, 2003. (ISBN: 1-85996-0545)

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