Hi Emmanuel, On Wed, 2013-02-13 16:30 EST, "Sampson, Jared" <jared.samp...@nyumc.org> wrote:
> You might consider using MSMS. If you wish to visualize it, there is a > PyMOL script available: http://pymolwiki.org/index.php/Msms. > > Relatedly, one should keep in mind that, while a 10 or 50 Angstrom probe > will give you a general idea of accessible surface, if there is any shape > complimentarity between two interacting proteins, it won't provide the > whole picture. I would second Jared's suggestion of MSMS. It is straightforward to set up a script to calculate the areas for each atom at many different probe radii. Note that when run with a very large probe size, the calculation takes substantially longer -- total run times on a protein of 185 residues takes less than a second for radii up to 15 A, but increases to 5 minutes for a 20 A probe radius. I didn't bother trying a 50 A probe. MSMS when run with the "-af" option will generate a file containing the accessible areas for each atom. I have several python scripts that will calculate total areas for various atom classes (hydrophobic, charged, etc.) and also save an output file with areas for each atom and/or residue. These can be run from within PyMOL or as standalone scripts. Similar to the script Jared mentions, my msms_pymol.py script will also allow visualization of the MSMS surface in PyMOL. My various python scripts can be found here: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ Cheers, Rob >> On Feb 12, 2013, at 2:51 PM, Emmanuel Levy >> <emmanuel.l...@gmail.com<mailto:emmanuel.l...@gmail.com>> wrote: >> >> Hello, >> >> I have been looking for a tool to measure the "Protein accessible >> surface area", which could be defined exactly as the solvent ASA >> except with a probe of larger radius. >> >> Most tools that calculate ASA however do not work with a probe radius >> of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to >> know the "largest probe size that can access each atom or residue". So >> using classic ASA programs means one would have to run it ~30 times, >> each time with different probe radius for each protein. >> >> So my question is, do you know of a tool that could help us in >> obtaining this type of information? >> >> Thanks in advance for any hint, >> All the best, >> >> Emmanuel -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
