Statistics for BioGeometry Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Aug 2024 412 ...

TOC Misc papers on hydrogen bonds Ask me for any papers that aren't already linked/attached. Link back to: RosettaHydrogenBonds Survey E. N. BAKER and R. E. HUBBARD ...

Place to jot ideas Plot percentage of density to evaluate which candidates really ore H bonds. Measure lengthen of bifurcated bonds. Correlate H bond lengths at surface ...

Running OptE on UNC clusters: OptEOnTopsail OptEOnBass HbondPapers ResearchIdeasJotPad Previous work by Chris Sheldahl: Main.ChrisProgress Implemented ideas to ImproveHbonds ...

UNC getting started on Topsail page http://help.unc.edu/6214 Load the gcc development suit module module load hpc/mvapich-gcc get mini source onto the scratch partition ...

A protocol for fitting the weights of the energy function Documentation for OptE INTRODUCTION OptE is a protocol for optimizing the weights of the score function ...

The Biogeometry wiki is a collection of random pages from those of use here at UNC Computer Science who are interested in geometric problems arising in structural ...

BioGeometry Web Preferences The following settings are web preferences of the BioGeometry web. These preferences overwrite the site-level preferences in TWIKIWEB ...

Phil Bradley has done some preliminary work on including explicit waters into rosetta. I will begin by looking at his work with the goal of being able to present ...

Site Tools of the BioGeometry Web INCLUDE{" TWIKIWEB .WebSiteTools"} Notes: INCLUDE{" TWIKIWEB .YouAreHere"} Main.ChristianStith 03 Jul 2008

Please visit previous revision. TOC Please add events, or move expired events to Main.EventsArchive. Speakers WEDNESDAY, APRIL 26 "Structural Investigations of Protein ...

Please add your information or email me (snoeyink@cs.unc.edu) to add it. The meeting will take place at the Cheeca Lodge in Islamorada, Florida, on Tuesday, Wednesday ...

These are the backbone residues Brian Kuhlman suggested for modification in the meeting of Jan 4, 2006. The pdb files and PyMol scenes are in designDecoyResidueSelections ...

TOC Planned meetings 6 Dec: Glenn Butterfoss Brian Kuhlmann, more on protein voids Past meetings 22 Nov: Craig Bennetts Jack Snoeyink, estimating protein voids We ...

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 ...

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 ...

TOC RNA Secondary Structure Prediction The problem of predicting the RNA Secondary Structure without pseudoknots is well-resolved 1-6 , with time O(n3) and space ...

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 ...

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

We say that a graph G satisfies a Laman condition for 3d if every induced subgraph (V,E) with V 2 satisfies 3 V 6 E . Jacobs claimed that a graph was rigid in 3d ...

Here are some rigidity questions that we are working on: ProteinAllostery: can rigidity analysis for some set of bonds give a model for an allosteric interaction ...

I've recently obtained the book "Molecular Driving Forces" by Dill Bromberg, which introduces statistical thermodynamics and all the associated mathematics. It is ...

I presented Sariel Har-Peled's slides on well-separated pair decompositions in group meeting today. They have links to Callahan Kosaraju's paper. See also the Multipole ...

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

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 ...

This question is partially addressed in RotamerTrie Main.JackSnoeyink 02 Apr 2005 Rotamer Energy Calculation Main.AndrewLeaverFay 21 Feb 2005 Problem: minimize ...

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 ...

Main.AndrewLeaverFay 21 Feb 2005 Rotamer Energy Calculation Problem: minimize the number of additions and table-look-ups in calculating the pair interaction energy ...

Using Manocha's 6dof solver for protein backbone manipulation. Main.JackSnoeyink 04 Feb 2005 r6solver.zip: Dump of all tools in directory no warranty

a collection of matlab functions to read proteins from pdb format and calculate parameters. pdbread read a pdb file with optional het atoms selectAmino chooses ...

Here are some things that we have written in MATLAB for working with protein structures. PdbTools read pdb files, do Ramachandran plots, rmsd, etc. Idiosyncratic ...

INCLUDINGWEB Web INCLUDINGWEB Web Home Events Main.ProgressReports Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" ...

A place to paste expired events. Main.JackSnoeyink 04 Feb 2005

This is a subscription service to be automatically notified by e-mail when topics change in this BioGeometry web. This is a convenient service, so you do not have ...

TWiki's BioGeometry web SCRIPTURL /view SCRIPTSUFFIX /BioGeometry The BioGeometry web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World ...

INCLUDE{" TWIKIWEB .WebSearchAdvanced"}

SEARCH{"\. " scope "topic" regex "on" nosearch "on"} See also the faster WebTopicList

TOPICLIST{" $name "} See also the verbose WebIndex.

INCLUDE{" TWIKIWEB .WebChanges"}

INCLUDE{" TWIKIWEB .WebSearch"}