| Topics in BioGeometry web: | Changed: now 01:06 | Changed by: |
| DarpaFL06 | 15 Mar 2006 - 10:32 - NEW | JackSnoeyink |
| 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 ... | ||
| EventsArchive | 04 Feb 2005 - 13:09 - NEW | JackSnoeyink |
| A place to paste expired events. Main.JackSnoeyink 04 Feb 2005 | ||
| EventsCalendar | 26 Apr 2006 - 15:43 - r1.11 | JackSnoeyink |
| Please visit previous revision. TOC Please add events, or move expired events to Main.EventsArchive. Speakers WEDNESDAY, APRIL 26 "Structural Investigations of Protein ... | ||
| ExplicitWaterRefactor | 11 Jul 2005 - 15:44 - NEW | AndrewLeaverFay |
| Main.AndrewLeaverFay 11 Jul 2005 Rosetta adds extra rotamers with explicitly attached water molecules. These rotamers duplicate side chain dihedrals / atom coordinates ... | ||
| HbondPapers | 21 Jul 2009 - 18:56 - r1.3 | JackSnoeyink |
| 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 ... | ||
| ImpliedHinges | 24 Jun 2005 - 13:47 - r1.7 | AndreaMantler |
| 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 if ... | ||
| ImproveHbonds | 26 Mar 2005 - 13:00 - r1.2 | JackSnoeyink |
| 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 ... | ||
| LiteratureReviews | 07 Sep 2005 - 17:59 - r1.11 | XueyiWang |
| 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 ... | ||
| MatlabScripts | 04 Feb 2005 - 14:58 - NEW | JackSnoeyink |
| 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, ... | ||
| MolecularDrivingForces | 27 May 2005 - 12:18 - r1.2 | JackSnoeyink |
| I've recently obtained the book "Molecular Driving Forces" by Dill Bromberg, which introduces statistical thermodynamics and all the associated mathematics. It is ... | ||
| OpenProblems | 22 Feb 2005 - 10:33 - r1.2 | JackSnoeyink |
| Main.AndrewLeaverFay 21 Feb 2005 Rotamer Energy Calculation Problem: minimize the number of additions and table-look-ups in calculating the pair interaction energy ... | ||
| OptE | 04 Feb 2009 - 17:03 - r1.2 | MatthewOmeara |
| 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 ... | ||
| OptEOnTopsail | 11 Feb 2009 - 18:00 - r1.8 | MatthewOmeara |
| 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 ... | ||
| OptimizingRosetta | 23 Nov 2005 - 16:45 - r1.5 | JackSnoeyink |
| 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 ... | ||
| PdbTools | 04 Feb 2005 - 15:03 - NEW | JackSnoeyink |
| 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 just ... | ||
| ProjectIdeas | 02 Sep 2005 - 13:27 - r1.5 | JackSnoeyink |
| 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 ... | ||
| ProteinVoid | 23 Nov 2005 - 16:53 - NEW | JackSnoeyink |
| 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 ... | ||
| R6Solver | 04 Feb 2005 - 15:06 - NEW | JackSnoeyink |
| Using Manocha's 6dof solver for protein backbone manipulation. Main.JackSnoeyink 04 Feb 2005 r6solver.zip: Dump of all tools in directory no warranty | ||
| ResearchIdeasJotPad | 21 Jul 2009 - 18:19 - NEW | JackSnoeyink |
| 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 ... | ||
| RigidityQuestions | 14 Jun 2005 - 09:26 - NEW | JackSnoeyink |
| 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 in ... | ||
| RosettaHydrogenBonds | 21 Jul 2009 - 18:16 - r1.6 | JackSnoeyink |
| Running OptE on UNC clusters: OptEOnTopsail OptEOnBass HbondPapers ResearchIdeasJotPad Previous work by Chris Sheldahl: Main.ChrisProgress Implemented ideas to ImproveHbonds ... | ||
| RosettaMeetings | 29 Nov 2005 - 21:56 - r1.5 | JackSnoeyink |
| 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 ... | ||
| RotamerEnergyCalculation | 02 Apr 2005 - 13:21 - NEW | JackSnoeyink |
| This question is partially addressed in RotamerTrie Main.JackSnoeyink 02 Apr 2005 Rotamer Energy Calculation Main.AndrewLeaverFay 21 Feb 2005 Problem: minimize ... | ||
| RotamerTrie | 13 Apr 2005 - 09:59 - r1.7 | JackSnoeyink |
| 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 ... | ||
| RotamerWaters | 05 Sep 2008 - 20:51 - NEW | JackSnoeyink |
| 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 ... | ||
| SiteTools | 03 Jul 2008 - 15:22 - NEW | ChristianStith |
| Site Tools of the BioGeometry Web INCLUDE{" TWIKIWEB .WebSiteTools"} Notes: INCLUDE{" TWIKIWEB .YouAreHere"} Main.ChristianStith 03 Jul 2008 | ||
| SpeedSimulatedAnnealing | 25 Apr 2005 - 13:59 - NEW | AndrewLeaverFay |
| Main.AndrewLeaverFay 25 Apr 2005 In the rotamer substitution step of simulated annealing, Rosetta calculates the energy difference a rotamer substitution would ... | ||
| SuperRotamers | 04 Jan 2006 - 22:24 - NEW | JackSnoeyink |
| 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 ... | ||
| UseInitializers | 13 Apr 2005 - 10:10 - NEW | JackSnoeyink |
| 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 | ||
| WebChanges | 16 Aug 2001 - 19:58 - NEW | PeterThoeny |
| INCLUDE{" TWIKIWEB .WebChanges"} | ||
| WebHome | 04 Feb 2009 - 16:11 - r1.15 | MatthewOmeara |
| 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 ... | ||
| WebIndex | 24 Nov 2001 - 11:41 - r1.2 | PeterThoeny |
| SEARCH{"\. " scope "topic" regex "on" nosearch "on"} See also the faster WebTopicList | ||
| WebLeftBar | 04 Feb 2005 - 13:48 - r1.2 | JackSnoeyink |
| INCLUDINGWEB Web INCLUDINGWEB Web Home Events Main.ProgressReports Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" ... | ||
| WebNotify | 28 Aug 2004 - 07:30 - r1.4 | PeterThoeny |
| 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 ... | ||
| WebPreferences | 28 Jan 2009 - 19:17 - r1.12 | JackSnoeyink |
| BioGeometry Web Preferences The following settings are web preferences of the BioGeometry web. These preferences overwrite the site-level preferences in TWIKIWEB ... | ||
| WebRss | 16 Aug 2004 - 03:27 - r1.2 | PeterThoeny |
| TWiki's BioGeometry web SCRIPTURL /view SCRIPTSUFFIX /BioGeometry The BioGeometry web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World ... | ||
| WebSearch | 08 Aug 2001 - 05:26 - NEW | PeterThoeny |
| INCLUDE{" TWIKIWEB .WebSearch"} | ||
| WebSearchAdvanced | 18 Jan 2004 - 10:52 - NEW | PeterThoeny |
| INCLUDE{" TWIKIWEB .WebSearchAdvanced"} | ||
| WebStatistics | 02 Aug 2024 - 22:15 - r1.13 | Main.guest |
| 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 ... | ||
| WebTopicList | 24 Nov 2001 - 11:40 - NEW | PeterThoeny |
| TOPICLIST{" $name "} See also the verbose WebIndex. | ||
| WellSeparatedPairDecomposition | 28 Apr 2005 - 21:16 - NEW | JackSnoeyink |
| 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 ... | ||