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Nucleic Acids Research Advance Access published online on May 5, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp304
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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RASMOT-3D PRO: a 3D motif search webserver

Gaëlle Debret1, Arnaud Martel2 and Philippe Cuniasse1,*

1Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) and 2Groupe informatique pour les scientifiques d'Ile-de-France (GIPSI), iBiTec-S, DSV, CEA, CE-Saclay, 91191 Gif Sur Yvette Cedex, France

*To whom correspondence should be addressed. Tel: +331 69 08 56 35; Fax: +331 69 08 90 71; Email: philippe.cuniasse{at}cea.fr

Received January 30, 2009. Revised April 8, 2009. Accepted April 16, 2009.

Detection of structural motif of residues in protein structures allows identification of structural or functional similarity between proteins. In the field of protein engineering, structural motif identification is essential to select protein scaffolds on which a motif of residues can be transferred to design a new protein with a given function. We describe here the RASMOT-3D PRO webserver (http://biodev.extra.cea.fr/rasmot3d/) that performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology. Comparison is based on C{alpha} and Cβ atoms in two steps: inter-atomic distances and RMSD. RASMOT-3D PRO takes in input a PDB file containing the 3D coordinates of the searched motif and provides 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 in those deposited in the PDB. This characteristic as well as the possibility to reject scaffolds sterically incompatible with the target, makes RASMOT-3D PRO a unique webtool in the field of protein engineering.


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