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

* 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

-- JackSnoeyink - 20 Sep 2005

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