Dear Sarah, we don't have a server for you to quickly use but our lab has methods for alignment-free binding sites comparison by comparing pocket surface shape, named Pocket-Surfer and Patch-Surfer.
These are literature: http://www.ncbi.nlm.nih.gov/pubmed/20455259 http://www.ncbi.nlm.nih.gov/pubmed/22275074 http://bioinformatics.oxfordjournals.org/content/early/2014/10/29/bioinformatics.btu724.abstract If you are interested, I am happy to discuss what we can do for your problem. Sincerely, Daisuke ---- Daisuke Kihara, Ph.D. Professo Department of Biological Sciences/Computer Science Purdue University West Lafayette, IN 47907 http://kiharalab.org Tel: 1-765-496-2284 On Fri, Oct 31, 2014 at 3:48 PM, Sarah Barelier < [email protected]> wrote: > Dear all, > I'm sorry, this is a bit off-topic. I'm looking for a tool to compare > pairs of binding sites. > It doesn't need to be high-throughput, since I'll only be comparing ~100 > pairs, but I'd like it to be robust and, more importantly, > alignment-independent. > Indeed, the binding sites I want to compare are not necessarily related in > terms of amino-acid composition, but I'd like to still be able to detect > similarities between them. > Does anyone have suggestions? > Thank you. > > Sarah > > -- > Sarah Barelier, Ph.D. > Postdoctoral Researcher > Shoichet Lab, UCSF > [email protected] > > Department of Pharmaceutical Chemistry > 1700 4th Street, Byers Hall, Room N501 > San Francisco, CA 94158-2550 > -- Daisuke
