Sunday, June 17, 2007

Deciding which Fragment is Flexible or not on MolmovDB

We want to know which fragment is flexible or not according to the information from “the molmovdb” database.

If your protein has been crystallized in two conformations you can submit a job to our "morph server." Visual inspection may then give you the information you seek. If you have only one structure, you can submit it to our HingeMaster server, and several different flexibility analysis programs will be used to find the hinge location. Note that this is designed for use with domain hinge bending proteins. It will not be very helpful if your protein moves by shear or order-disorder transition mechanisms.

We also have a motion prediction program, the Conformation Explorer, which predicts conformational change for hinge bending proteins, either induced by ligand or otherwise. It's still under development, and use would require further discussion.

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