Skip to topic
|
Skip to bottom
Jump:
BioGeometry
BioGeometry Web
BioGeometry Web Home
Events
ProgressReports
Changes
Index
Search
Webs
BioGeometry
Main
TModeling
TWiki
Edit
Attach
Printable
BioGeometry.RosettaMeetings
r1.1 - 29 Nov 2005 - 21:56 - Main.guest
topic end
Start of topic |
Skip to actions
%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 report on the estimation of void volumes in protein and the feasibility of incorporating a measure of void volume into simulated annealing for protein design. The definition of void volumes as we compute them is: Put the protein in a grid of candidate waters and eliminate any waters whose standard spheres (default 1.4A) overlap the van der Waals spheres of atoms. Then estimate the volume of void space by counting the points in finer grid of candidate voids that are not contained in water or in atom spheres. We report estimated values for different grid spacings and perturbations for a native and designed example of 1bbz; if you want to bring any other protein pdb files, we can evaluate them as well. ---+++ 8 Nov: Yi Liu, scientific server ---+++ 18 Oct: Andrew Leaver-Fay, interaction graphs ---+++ 4 Oct: Deanne Sammond Binding, affinity & non-pairwise energy * [[%ATTACHURL%/omp_class_pres_10_3.ppt][omp_class_pres_10_3.ppt]]: Deanne's slides ---+++ 20 Sept, Jenny Hu Alternate backbones At this point, what I did is to 1.read in alternate backbone coordinate,"read_alternate_backbone"( in source.cc) 2.calculate torsion angle for families of backbone "ang_from_mpdb(source.cc)" 3.build alternate rotamers for each backbone "get_rotamers_mpdb(source.cc)" 4.alternate_backbone.cc is just used for building an backbone object ---+++ 30 Aug: Jack Snoeyink, hydrogen bonds I discussed Rosetta's current answer to the question, "What is a hydrogen bond?" and also some of the things we can do to ImproveHbonds. Part of the answer comes from: An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Kortemme T, Morozov AV, Baker D. J Mol Biol. 2003 Feb 28;326(4):1239-59. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12589766 -- Main.JackSnoeyink - 20 Sep 2005
to top
End of topic
Skip to action links
|
Back to top
Edit
|
Attach image or document
|
Printable version
|
Raw text
|
More topic actions
Revisions: | r1.1
|
Total page history
|
Backlinks
You are here:
BioGeometry
>
RosettaMeetings
to top
Copyright © 1999-2024 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding TWiki?
Send feedback