3D Structure Superposition

ebisu group

chemogenomix © 2012

Read more below


After you have an alignment you will probably want to generate a superposition of your structures to view in 3D.

ProFit was designed by Andrew Martin to be the ultimate protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc.

Some comments from users:

A user from Cambridge
Just downloaded ProFit on the recommendation of a colleague and got the answer I wanted within 5 minutes, what a fantastic program, easy to 'install' and elegant and simple syntax (can you tell I'm not used to this!!!).

A user from Los Alamos
Following the instructions in the on-line documentation, I was able to quickly compute the rmsd between structures in two pdb files.... Thank you for offering this program for use by the research community.

A user from the University of Chicago
Thanks a lot for writing such an useful piece of software and more importantly for documenting it and providing it for our use.

And if you do not want to install there is a free web site too:


Source Code, Linux binary, Windows binary

Freely available to all users direct from Andrew Martin’s web site at UCL.