PRince: a web server for structural and physicochemical analysis of Protein-RNA interface

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein–RNA interface. Users need to submit a PDB file contain-ing the atomic coordinates of both the protein and the RNA molecules in complex form (in ‘.pdb’ format). They should also mention the chain identi-fiers of interacting protein and RNA molecules. The size of the protein–RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein–RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters gen-erated by the server are presented in a tabular format. The interacting surfaces can also be vis-ualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic co-ordinates of the interacting protein, RNA and inter-face water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical param-eters for better understanding the specificity of the protein–RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free fo