Folding Forum

Project moderators: dsglazer and gwtang

Projects 10303 - 10306 are entering the advanced stage of testing, following in foot steps of projects 10300 and 10301. They also consist of several calcium binding structures each that are being simulated with several force fields in explicit solvent. Please see project description pages for more information.

WARNING:
The server code with which we are running these projects does not support generation of psummary entries. Please find project descriptions on the following pages:

http://fah-web.stanford.edu/cgi-bin/fah ... ed?p=10303
http://fah-web.stanford.edu/cgi-bin/fah ... ed?p=10304
http://fah-web.stanford.edu/cgi-bin/fah ... ed?p=10305
http://fah-web.stanford.edu/cgi-bin/fah ... ed?p=10306

The new projects use the CPU double precision GROMACS Fahcore. They are running from server 171.67.108.38.

Project 10303
Points 160
Timeout 31
Deadline 46

Project 10304
Points 175
Timeout 34
Deadline 50

Project 10305
Points 132
Timeout 26
Deadline 38

Project 10306
Points 145
Timeout 28
Deadline 42

Several more projects relating to these will follow soon.

dsglazer
Pande Group Member

Posts: 17
Joined: Tue Mar 30, 2010 12:13 am

Nice project description! The discussion of the experimental design, interesting in its own right, could also be useful to mods in the unlikely event that one of the sub-studies runs into computational problems.

The graphic is also particularly elegant. Are the strands in the "bundle of hair" the ensemble of final folded structures within a given interval of free energy from the absolute minimum? (Can't help wondering how the bundle-width varies with T, and why it looks so uniform everywhere, well, except at the ends) And it only just now struck me that the coloration represents physical distance along the protein between the C-terminal and N-terminal ends. This must be old-hat to protein-structure experts but to the rest of us, it's original and thought-provoking.

Thank you for the positive feedback. The strands in the "bundle of hair' represent backbones of structures generated by molecular dynamics simulations started from an already folded structure. So effectively, they are a short exploration of the conformational space of the molecule around a local (potentially absolute) free energy minimum for this particular structure. We don't have a sense of how the bundle-width varies with T, because we have not performed such an experiment. The uniformity in the image may come intrinsically from the structure itself, which consists of four interacting alpha-helices and intermittent loops arranged somewhat symmetrically. The starting structure, 1B9A from the PDB, in-fact, is made up of two EF-hands slightly offset from one another by rotation.