: Subject: Re: [ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?
My knowledge on this is probably quite out of date by now, but some years ago there was a lot of research on this topic because such surfaces are important in electrostatics and implicit solvation models (calculating surface area) as well as molecular graphics. I think the most widely-used definition of a solvent-accessible surface is Lee-Richards surface in which a solvent-sized sphere is rolled along the surface of the protein. Surface is therefore rigorously defined as a piecewise collection of convex and concave patches of spheres and tori. It was Connolly who implemented (and sold) a practical algorithm for computing these surfaces. They were even known as Connolly surfaces and rendered as dots before modern computing hardware allowed for rendering surfaces. Several groups have developed high-efficiency versions of the calculation. Harold Scheraga's group, for example, has some FORTRAN code for this. Fred Brook's virtual reality group also developed a high-effeciency parallel version (Varshney was the guy's name I think) in C. There have been many approximations over the years I think ... but you asked about analytical models. The these algorithms are non trivial. That's a understatement. And there is actually a mathematical ambiguity in the surface definition itself. The Varshney code is freely available ... I received email permission from both Varshney and his thesis advisor to freely distribute the code. I even offered it to Warren Delano years ago when he was writing Pymol, but he refused to include it because he felt there still might be legal issues that would effect Pymol. So ... Pymol contains only a somewhat improvised an non-rigorous surface algorithm (last time I looked). Fine for graphics of course. en.wikipedia.org/wiki/Accessible_surface_area<http://en.wikipedia.org/wiki/Accessible_surface_area> Richard On Jan 13, 2011, at 1:00 AM, Francois Berenger wrote: Hello, Does someone know some good articles on this particular topic? I'd like to implement the thing myself, however if there is a good software doing the job (with readable source code), I might use and cite it. Best regards, Francois.
