Main.AndrewLeaverFay 11 Jul 2005 Rosetta adds extra rotamers with explicitly attached water molecules. These rotamers duplicate side chain dihedrals / atom coordinates ...

TOC Here are some ways to improve hbonds.cc from OptimizingRosetta. hbonds.cc: original hbonds.cc The energy function The function used comes from Kortemme et al ...

Here are some ideas for optimizing Rosetta, with links to new pages for the ones that we actually experiment on, or carry out. RotamerTrie store rotamer sets in a ...

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 ...

TOC Estimating protein void volumes Question: is it worthwhile putting in an estimate of the void volume as part of the energy function for optimizing rotamer choices ...

A topic under OptimizingRosetta TOC We should try to submit to WABI, April 20. This will take some work... The basic idea is described in Hellinga's paper, so we need ...

Main.AndrewLeaverFay 25 Apr 2005 In the rotamer substitution step of simulated annealing, Rosetta calculates the energy difference a rotamer substitution would ...

http://msdn.microsoft.com/library/en-us/vccelng/htm/ators 17.asp http://www.devx.com/getHelpOn/Article/16039/1954?pf true Main.JackSnoeyink 13 Apr 2005

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