Recursive Automatic Search of MOTif in 3D structures of PROteins

RASMOT-3D PRO: FAQ

RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by the motif given in input. Comparison is based on Ca and Cb atoms in two steps: inter-atomic distances comparison and root mean square deviation. The result is an interactive list of identified protein structures exhibiting residues of similar topology as the motif searched. Each solution can be graphically examined on the website. The topological search can be conducted in structures described in PDB files uploaded by the user or deposited in the PDB. This characteristics as well as the possibility to reject scaffolds sterically incompatible with a target, make RASMOT-3D PRO a unique webtool in the field of protein engineering.

You can not directly download RASMOT-3D PRO. However, a more elaborated version of the program is available on demand. Please contact the coordinator.

This method uses exhaustive rotamers search to select proteins that can reproduce the topology of functional groups in residues (e.g. NZ atom of Lysine can form a bond. To reproduce this bond, the Lysine backbone can be in different positions). Automatic interface analysis can be performed to select groups of functional residues. This method also allows searching for sub-groups residues. The search can be achieved in the full PDB database, setting up several parameters to refine the solutions. These options render the search more efficient but necessitate high amount of computational facilities.

Only PDB format is allowed. The Protein Data Bank (PDB) format provides a standard representation for macromolecular structure data derived from X-ray diffraction and NMR studies.
Only ATOM records, which contains the atoms specifications, are read by RASMOT- 3D PRO. For a complete description of the ATOM record format, see the Protein Data Bank Contents Guide .

RASMOT-3D PRO runs on the server. You do not have to install anything to run a job. However, Jmol Applet is used to visualize the 3D structures of the solution proteins. It is integrated into webpages and does not require any plugin installation. Jmol only requires Java installation (http://www.java.com/) and operates on a wide variety of platforms.

If you publish work in which you have used RASMOT-3D PRO, please cite the following publication:

Magis C, Gasparini D, Lecoq A, Le Du MH, Stura E, Charbonnier JB, Mourier G, Boulain JC, Pardo L, Caruana A, Joly A, Lefranc M, Masella M, Menez A, Cuniasse P., Structure-based secondary structure-independent approach to design protein ligands: Application to the design of Kv1.2 potassium channel blockers. 2006 Dec 20;128(50):16190-205 pubmed

RASMOT-3D PRO policy is to respect and protect the privacy of our users. All collected informations (e-mail adress, uploaded structure files) are considered confidential.
We do not sell, trade, nor give away informations to other organizations. All uploaded informations are destroyed from our servers after 1 day.