algorithmsforconformationalanalysisoflongproteinloops.pptVIP

Geometric Algorithms for Conformational Analysis of Long Protein Loops J. Cortess, T. Simeon, M. Remaud-Simeon, V. Tran Motivation Filter unfeasible loop conformations to aid searching conformational space for various application: Protein loop modeling Molecular simulations: conformational changes under environmental conditions. Structural Constraints Loop-closure Steric clash – internal segment clashes (self-clashes), external clashes, VdW radii. Loop Closure Approaches Analytical – IK techniques Optimization – e.g. CCD Database based methods Clash Filtering Approaches Energetic – accepting/r