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423f11-scp - Side-Chain Positioning CMSC 423 Protein...

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Side-Chain Positioning CMSC 423
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Backbone Protein Structure
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Backbone Protein Structure Side-chains
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Side-chain Positioning Given: - amino acid sequence - position of backbone in space Find best 3D positions for side chains “Best” = lowest-energy Discrete formulation reasonable using rotamers
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Side-chain Positioning Problem Given: fixed backbone amino acid sequence Find the 3D positions for the side-chains that minimize the energy of the structure Assume lowest energy is best IILVPACW…
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3 rotamers of Arg
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Applications Homology modeling Rapid, low-cost structure determination Protein design Find sequence that folds into a given shape e.g. redesign of zinc finger that folds without zinc, (Dahiyat+97) Ligand binding e.g. novel binding pockets (Looger+03) Subroutine in flexible backbone prediction e.g. (Bradley+,2005) D
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Graph Problem Graph with part V i for each side chain: node for each rotamer edge {u,v} represents the interaction between u and v Weights: E(u) = self-energy E(u,v) = interaction energy rotamer residue interaction V 1 V 2
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Graph Problem Solution is one node from each part
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