Analysis and Prediction of Protein Structure - Eagle.cs.missouri.edu ...

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Outline I. Sequence, Structure, Function Relation II. III. IV. Determination, Storage, Visualization, Analysis, and Comparison Structure Classification 1D Prediction V. 2D Prediction VI. 3D Prediction VII. Useful Tools
Protein Structure Determination • X-ray crystallography • Nuclear Magnetic Resonance (NMR) Spectroscopy • X-ray: any size, accurate (1-3 Angstrom (10 -10 m)), sometime hard to grow crystal • NMR: small to medium size, moderate accuracy, structure in solution
Page 1 and 2: Analysis and Prediction of Protein
Page 3 and 4: Sequence, Structure and Function AG
Page 5 and 6: Amino Acids Hydrophilic
Page 7 and 8: Protein Secondary Structure • Det
Page 9 and 10: Beta-Sheet Anti-Parallel Parallel
Page 11 and 12: Tertiary Structure • John Kendrew
Page 13: Anfinsen’s Folding Experiment •
Page 18 and 19: Wikipedia, the free encyclopedia
Page 20: Storage in Protein Data Bank Search
Page 23 and 24: J. Pevsner, 2005
Page 25 and 26: Protein Structure Classification
Page 27 and 28: Colors in the universe of protein s
Page 29 and 30: Another Fold Example: TIM betaalpha
Page 31 and 32: Fold: beta barrel http://scop.berke
Page 33: SCOP Classification Levels SCOP Roo
Page 36 and 37: Goal of structure prediction • Ep
Page 38 and 39: 1D: Secondary Structure Prediction
Page 40 and 41: Secondary Structure Prediction Sing
Page 42 and 43: Helix formation is local THYROID ho
Page 44 and 45: . . . S D R Q G F V P A A Y V K K P
Page 46 and 47: Comments: frequency is often normal
Page 48 and 49: Useful Tools • PSI-PRED (http://b
Page 50 and 51: 2D: Contact Map Prediction 3D Struc
Page 52 and 53: Main Contact Prediction Tools Tegge
Page 54 and 55: Outline I. Sequence, Structure, Fun
Page 56 and 57: Two Approaches •Ab Initio Structu
Page 58 and 59: Protein Energy Landscape
Page 60 and 61: Some Ab Initio Tools • David Bake
Page 62 and 63: Template Identification • Sequenc
Page 64 and 65: Classic Fold Recognition Approaches
Page 66 and 67:
Classic Fold Recognition Approaches
Page 68 and 69:
Query-Template Pair Machine Learnin
Page 70 and 71:
Query-Template Alignment • Most f
Page 72 and 73:
A. Fisher, 2005
Page 74 and 75:
An PIR Alignment Example Template i
Page 76 and 77:
Modeller Python Script (bioinfo.py)
Page 78 and 79:
Model Evaluation • Prosa (http://
Page 80 and 81:
Outline I. Sequence, Structure, Fun
Page 82 and 83:
Protein Folding Game: FoldIt • Vi
Page 84:
Assignment (Review one paper) • Y
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