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BioGeometry.ProjectIdeas
r1.1 - 02 Sep 2005 - 13:27 - Main.guest
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This is a place to jot down project ideas, and link to WikiWords for projects where the ideas are more fleshed out. * OptimizingRosetta for ideas specifically pertaining to the Rosetta code. * MageFlips: Jane Richardson wants us to calculate the cost of flips in mage so that it can be integrated into MolProbity. * Fast pruning of a tree-structured rotamers. We've implemented a RotamerTrie for Rosetta, now can we look at the general problem of rotamers that are structured as overlapping trees: * How can you quickly prune out those branches that will have intersections with backbone? Are there quick rejection tests that show that branches of a tree cannot fit into a small space? perhaps by computing the neighborhood of one atom and using that to prune sets of nodes from the tree. * If you place two tries next to each other, is there a way other than brute force to determine how they can fit tightly together -- perhaps by exploring separating planes? * A completely different way is to think of rotamer atoms as point clouds and evaluate energies of one point cloud against another by a WellSeparatedPairDecomposition. Does this give us energies any faster? * Baker's outside-in rotamers: How would we do rotamer tries starting from the tips (Baker's theozymes?) Given a collection of possible triples of Calpha positions of rotamers with fixed tips, how do we find a scaffold that can match the positions without clashing with the rotamers? * Ramachandran plots for RNA: what are the allowable ranges for angle parameters in the hard sphere model, and how do they compare to those observed by Berman's and the Richardsons' labs? * RigidityQuestions there are a number of hard rigidity questions, including the MolecularConjecture. -- Main.JackSnoeyink - 02 Apr 2005
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