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-us Copyright 2024 by contributing authors TWiki Administrator [snoeyink@unc.edu] TWiki Administrator [snoeyink@unc.edu] TWiki TWiki.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.gif https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/view.cgi/BioGeometry/WebStatistics?t=2024-08-11T03:17Z Statistics for BioGeometry Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Aug 2024 1230 ... (last changed by guest) 2024-08-11T03:17Z guest 1.14 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebStatistics https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebStatistics 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) 2009-07-21T18:56Z JackSnoeyink 1.3 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/HbondPapers https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/HbondPapers 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) 2009-07-21T18:19Z JackSnoeyink 1.1 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ResearchIdeasJotPad https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ResearchIdeasJotPad 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) 2009-07-21T18:16Z JackSnoeyink 1.6 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaHydrogenBonds https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaHydrogenBonds 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) 2009-02-11T18:00Z MatthewOmeara 1.8 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptEOnTopsail https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptEOnTopsail 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) 2009-02-04T17:03Z MatthewOmeara 1.2 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptE https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptE 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) 2009-02-04T16:11Z MatthewOmeara 1.15 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebHome https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebHome 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) 2009-01-28T19:17Z JackSnoeyink 1.12 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebPreferences https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/WebPreferences 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) 2008-09-05T20:51Z JackSnoeyink 1.1 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RotamerWaters https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RotamerWaters 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) 2008-07-03T15:22Z ChristianStith 1.1 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SiteTools https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SiteTools 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) 2006-04-26T15:43Z JackSnoeyink 1.11 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/EventsCalendar https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/EventsCalendar 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) 2006-03-15T10:32Z JackSnoeyink 1.1 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/DarpaFL06 https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/DarpaFL06 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) 2006-01-04T22:24Z JackSnoeyink 1.1 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SuperRotamers https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/SuperRotamers 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) 2005-11-29T21:56Z JackSnoeyink 1.5 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaMeetings https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/RosettaMeetings 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) 2005-11-23T16:53Z JackSnoeyink 1.1 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ProteinVoid https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/ProteinVoid 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) 2005-11-23T16:45Z JackSnoeyink 1.5 updated major https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptimizingRosetta https://wwwx.cs.unc.edu/Research/compgeom/twiki/bin/rdiff.cgi/BioGeometry/OptimizingRosetta
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