About 3d-SS

3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several three-dimensional protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures. The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed three-dimensional structures with the water molecules (invariant or common) in the client machine. Furthermore, an option is provided to save the superposed three-dimensional atomic coordinates in the client machine. To perform the above, users need to enter PDB-id(s) or upload the atomic coordinates in Protein Data Bank format. This server uses a locally maintained Protein Data Bank anonymous FTP server that is being updated weekly. This program can be accessed through our Bioinformatics web server at the URL http://cluster.physics.iisc.ernet.in/3dss/ or .