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

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Secondary Structure Prediction Single residues (Generation 1) (1. generation) – Chou-Fasman, GOR 1957-70/80 50-55% accuracy Secondary structure propensity score of an amino acid AA Log P(AA in Helix) / P(AA) Log P(AA in Sheet) / P(AA) Log P(AA in Loop) / P(AA)
Secondary Structure Prediction • Segments (window) • GOR III • Accuracy: 55-60% • 1986-1992 (Generation II) • Estimation: max < 65%, Strand: non-local, < 40% ARSKQPCTWYRESQTCEQRKRTPA Average propensity scores of a window
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 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 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 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 82 and 83: Protein Folding Game: FoldIt • Vi
Page 84: Assignment (Review one paper) • Y

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

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