Hi Emmanuel - 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. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 12, 2013, at 2:51 PM, Emmanuel Levy <[email protected]<mailto:[email protected]>> 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
