lecture19_S2009

lecture19_S2009 - April 22 nd , 2009 18.417 Lecture 20:...

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Unformatted text preview: April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 1/49 18.417: Comparative modeling and side-chain packing Charles W. ODonnell Slides courtesty Jrme Waldisphl, Jinbo Xu (TTI Chicago) April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 2/49 August 8 th , 2008 Science Bradley, et al, Proteins (2003) Bradley, et al, Proteins (2003) April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 3/49 Predictive accuracy slowing increasing April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 4/49 Distance between 3D structures April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 5/49 CASP/CAFASP CASP: C ritical A ssessment of S tructure P rediction CAFASP: C ritical A ssessment of F ully A utomated S tructure P rediction CASP Predictor CAFASP Predictor 1. Wont get tired 2. High-throughput April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 6/49 CASP/CAFASP Public Organized by structure community Evaluated by the unbiased third-party Held every two years Blind Experimental structures to be determined by structure centers after competition Drawback: <100 targets Blindness Some centers are reluctant to release their structures April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 7/49 April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 8/49 Test Protein Category New Fold (NF) targets No similar fold in PDB Homology Modeling (HM) targets Easy HM: has a homologous protein in PDB Hard HM: has a distant homologous protein in PDB Also called Comparative Modeling (CM) targets Fold Recognition (FR) targets Has a similar fold in PDB April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 9/49 Protein Structure Prediction Stage 1: Backbone Prediction Ab initio folding Homology modeling Protein threading Stage 2: Loop Modeling Stage 3: Side- Chain Packing Stage 4: Structure Refinement The picture is adapted from http://www.cs.ucdavis.edu/~koehl/ProModel/fillgap.html April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 10/49 Protein Structure Prediction Stage 1: Backbone Prediction Ab initio folding Homology modeling Protein threading Stage 2: Loop Modeling Stage 3: Side- Chain Packing Stage 4: Structure Refinement The picture is adapted from http://www.cs.ucdavis.edu/~koehl/ProModel/fillgap.html April 22 nd , 2009 18.417 Lecture 20: Comparative modeling and side-chain packing 11/49 Ab initio Prediction Sampling the global conformation space Lattice models / Discrete-state models Molecular Dynamics Pre-set libraries of fragment 3D motifs Picking native conformations with an energy function Solvation model: how protein interacts with water...
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lecture19_S2009 - April 22 nd , 2009 18.417 Lecture 20:...

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