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

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Protein Sequence N A directional sequence of amino acids/residues … C Amino Acid 1 Amino Acid 2 Peptide bond Side Chain Backbone
Protein Secondary Structure • Determined by hydrogen bond patterns • 3-Class categories: alpha-helix, betasheet, loop (or coil) • First deduced by Linus Pauling et al.
Page 1 and 2: Analysis and Prediction of Protein
Page 3 and 4: Sequence, Structure and Function AG
Page 5: Amino Acids Hydrophilic
Page 9 and 10: Beta-Sheet Anti-Parallel Parallel
Page 11 and 12: Tertiary Structure • John Kendrew
Page 13: Anfinsen’s Folding Experiment •
Page 16 and 17: Outline I. Sequence, Structure, Fun
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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