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pred3D - Prediction of protein structure aim Structure...

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Prediction of protein structure
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aim Structure prediction tries to build models of 3D structures of proteins that could be useful for understanding structure-function relationships.
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Genbank/EMBL 105.000.000 Uniprot 5.200.000 PDB 47.000 
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The protein folding problem The information for 3D structures is coded in the protein sequence Proteins fold in their native structure in seconds Native structures are both thermodynamically stables and kinetically available
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AVVTW...GTTWVR AVVTW...GTTWVR ab-initio prediction Prediction from sequence using first principles
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Ab-initio prediction “In theory”, we should be able to build native structures from first principles using sequence information and molecular dynamics simulations: “Ab-initio prediction of structure” Simulaciones de 1 μ s de “folding” de una proteína modelo (Duan-Kollman: Science, 277, 1793, 1998). Simulaciones de folding reversible de péptidos (20-200 ns) (Daura et al., Angew. Chem., 38, 236, 1999). Simulaciones distribuidas de folding de Villin (36-residues) (Zagrovic et al., JMB, 323, 927, 2002).
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... the bad news ... It is not possible to span simulations to the “seconds” range Simulations are limited to small systems and fast folding/unfolding events in known structures steered dynamics biased molecular dynamics Simplified systems
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typical shortcuts Reduce conformational space 1,2 atoms per residue fixed lattices Statistic force-fields obtained from known structures Average distances between residues Interactions Use building blocks: 3-9 residues from PDB structures
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Some protein from E Some protein from E .coli .coli predicted at 7.6 Å predicted at 7.6 Å (CASP3, H.Scheraga)
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