Superpose3D is a software for local structural comparison. It runs on Windows, Mac OSX and Linux and is released under the open source GPL license. Superpose3D was developed by Pier Federico Gherardini and Gabriele Ausiello. Protein structures, similarly to sequences, can be compared either globally, to reveal distant evolutionary relationships, or locally, to highlight similarities of specific group of residues such as enzyme active sites or ligand binding sites. Indeed two proteins can have similar functions even if their overall structures are completely different since the function depends on the position and identity of a small number of residues. Superpose3D allows you to uncover these small but crucial similarities between protein structures. You can use it to study ligand binding sites, enzyme active sites, protein/protein interaction surfaces etc. The main advantage of Superpose3D is that it allows you to specify in a completely flexible way how the structure is represented during the computation.
Name: Manuela Helmer Citterich