TWiki's BioGeometry web
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry
The BioGeometry web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World.en-usCopyright 2024 by contributing authorsTWiki Administrator [snoeyink@unc.edu]TWiki Administrator [snoeyink@unc.edu]TWikiTWiki.BioGeometryTWiki home.BioGeometry
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry
https://wwwx.cs.unc.edu/Research/compgeom/twiki/pub/TWiki/TWikiLogos/twikiRobot46x50.gifWebStatistics
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/WebStatistics?t=2024-09-03T09:59Z
Statistics for BioGeometry Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Sep 2024 81 0 ... (last changed by guest)2024-09-03T09:59Zguest1.18updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebStatisticshttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebStatisticsHbondPapers
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/HbondPapers?t=2009-07-21T18:56Z
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 ... (last changed by JackSnoeyink)2009-07-21T18:56ZJackSnoeyink1.3updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/HbondPapershttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/HbondPapersResearchIdeasJotPad
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/ResearchIdeasJotPad?t=2009-07-21T18:19Z
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 ... (last changed by JackSnoeyink)2009-07-21T18:19ZJackSnoeyink1.1updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ResearchIdeasJotPadhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ResearchIdeasJotPadRosettaHydrogenBonds
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/RosettaHydrogenBonds?t=2009-07-21T18:16Z
Running OptE on UNC clusters: OptEOnTopsail OptEOnBass HbondPapers ResearchIdeasJotPad Previous work by Chris Sheldahl: Main.ChrisProgress Implemented ideas to ImproveHbonds ... (last changed by JackSnoeyink)2009-07-21T18:16ZJackSnoeyink1.6updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaHydrogenBondshttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaHydrogenBondsOptEOnTopsail
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/OptEOnTopsail?t=2009-02-11T18:00Z
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 ... (last changed by MatthewOmeara)2009-02-11T18:00ZMatthewOmeara1.8updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptEOnTopsailhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptEOnTopsailOptE
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/OptE?t=2009-02-04T17:03Z
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 for ... (last changed by MatthewOmeara)2009-02-04T17:03ZMatthewOmeara1.2updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptEhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptEWebHome
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/WebHome?t=2009-02-04T16:11Z
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 ... (last changed by MatthewOmeara)2009-02-04T16:11ZMatthewOmeara1.15updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebHomehttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebHomeWebPreferences
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/WebPreferences?t=2009-01-28T19:17Z
BioGeometry Web Preferences The following settings are web preferences of the BioGeometry web. These preferences overwrite the site-level preferences in TWIKIWEB ... (last changed by JackSnoeyink)2009-01-28T19:17ZJackSnoeyink1.12updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebPreferenceshttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebPreferencesRotamerWaters
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/RotamerWaters?t=2008-09-05T20:51Z
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 ... (last changed by JackSnoeyink)2008-09-05T20:51ZJackSnoeyink1.1updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RotamerWatershttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RotamerWatersSiteTools
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/SiteTools?t=2008-07-03T15:22Z
Site Tools of the BioGeometry Web INCLUDE{" TWIKIWEB .WebSiteTools"} Notes: INCLUDE{" TWIKIWEB .YouAreHere"} Main.ChristianStith 03 Jul 2008 (last changed by ChristianStith)2008-07-03T15:22ZChristianStith1.1updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SiteToolshttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SiteToolsEventsCalendar
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/EventsCalendar?t=2006-04-26T15:43Z
Please visit previous revision. TOC Please add events, or move expired events to Main.EventsArchive. Speakers WEDNESDAY, APRIL 26 "Structural Investigations of Protein ... (last changed by JackSnoeyink)2006-04-26T15:43ZJackSnoeyink1.11updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/EventsCalendarhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/EventsCalendarDarpaFL06
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/DarpaFL06?t=2006-03-15T10:32Z
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 ... (last changed by JackSnoeyink)2006-03-15T10:32ZJackSnoeyink1.1updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/DarpaFL06https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/DarpaFL06SuperRotamers
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/SuperRotamers?t=2006-01-04T22:24Z
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 ... (last changed by JackSnoeyink)2006-01-04T22:24ZJackSnoeyink1.1updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SuperRotamershttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SuperRotamersRosettaMeetings
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/RosettaMeetings?t=2005-11-29T21:56Z
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 ... (last changed by JackSnoeyink)2005-11-29T21:56ZJackSnoeyink1.5updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaMeetingshttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaMeetingsProteinVoid
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/ProteinVoid?t=2005-11-23T16:53Z
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 ... (last changed by JackSnoeyink)2005-11-23T16:53ZJackSnoeyink1.1updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ProteinVoidhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ProteinVoidOptimizingRosetta
https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/OptimizingRosetta?t=2005-11-23T16:45Z
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 ... (last changed by JackSnoeyink)2005-11-23T16:45ZJackSnoeyink1.5updatedmajorhttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptimizingRosettahttps://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptimizingRosetta