RAPIDO is an algorithm for the 3D alignment of protein structures. In order to align your protein structures:.

  1. Choose the structures either by providing a comma separated list of PDB IDs or by uploading a zipped tarball of you PDB files (use the unix command: tar czvf tarball.tgz <list-of-pdb-files>).
  2. Insert your e-mail address. An email with a confirmation and a link for accessing the results will be sent to this e-mail address.1
  3. Press the submit button

A help page for RAPIDO is available here.

  File to upload:
  List of PDB IDs:
  Email address:

In citing RAPIDO please refer to:

Roberto Mosca, Barbara Brannetti, Thomas R Schneider, Alignment of protein structures in the presence of domain motions, BMC Bioinformatics 2008, 9:352, doi:10.1186/1471-2105-9-352 [link]

Roberto Mosca, Thomas R. Schneider, RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes, Nucleic Acids Research 2008; doi: 10.1093/nar/gkn197 [link]


RAPIDO. Software for the structural alignment of protein structures in the presence of conformational changes.

Copyright 2005-2006 FIRC Institute of Molecular Oncology (IFOM)
Copyright 2005-2006 European Institute of Oncology (IEO)
Copyright 2007-2008 European Molecular Biology Laboratory (EMBL)

RAPIDO was developed by T.R. Schneider and R. Mosca at the FIRC Institute of Molecular Oncology, European Institute of Oncology and EMBL Hamburg.
The development of RAPIDO was supported by a grant from the Associazione Italiana per la Ricerca sul Cancro (AIRC).

Pages on this server were created by Roberto Mosca (roberto.mosca at embl-hamburg.de) and Thomas R. Schneider (thomas.schneider at embl-hamburg.de). RM and TRS accept full responsibility for the content of these pages, for which EMBL is not responsible by any means.

Last Edited: 09 June 2008


(1) The results will be kept on the server for at least 48 hours under a randomly generated URL directly accessible from outside. The provider of this service will not be liable for any direct, indirect or consequential loss or damage arising from a unauthorized access to the data.

For questions and suggestions please write to rapido@embl-hamburg.de.