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Simplified representation Fast Novel solvent model Extensible

Poing. A dynamic model of protein folding. Simplified representation Fast Novel solvent model Extensible. Poing. Small hydrophilic sidechain. structure simplification. Backbone C-alpha. Protein backbone. Large hydrophobic sidechain. Poing. linear elastic springs. Poing.

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Simplified representation Fast Novel solvent model Extensible

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  1. Poing A dynamic model of protein folding • Simplified representation • Fast • Novel solvent model • Extensible

  2. Poing Small hydrophilic sidechain structure simplification Backbone C-alpha Protein backbone Large hydrophobic sidechain

  3. Poing linear elastic springs

  4. Poing Langevin dynamics is F = ma ... PLUS a model for solvent a: acceleration F: net force (sum of many forces) γ: drag factor v: current particle velocity R: randomly distributed vector m: particle mass

  5. Poing Secondary structure and hydrogen bonding Solvent model leads tohydrophobic collapse Sidechain size and shape

  6. Phyre + Poing HMM ARNDLSLDLVCS……. PSI-Blast Hidden Markov Model DB of KNOWN STRUCTURES HMM-HMM matching FINAL MODEL POING: Synthesise from virtual ribosome. Springs for constraints. Ab initio modelling of missing regions. Extract pairwise distance constraints

  7. Protein Folding Requires Crowd Control in a Simulated Cell. Jefferys BR, Kelley LA and Sternberg MJE Journal of Molecular Biology (2010) Volume 397, Issue 5, 16 April 2010, Pages 1329-1338

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