title: RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes.
abstract: Rapid alignment of proteins in terms of domains (RAPIDO) is a web server for the 3D alignment of crystal structures of different protein molecules in the presence of conformational change. The structural alignment algorithm identifies groups of equivalent atoms whose interatomic distances are constant (within a defined tolerance) in the two structures being compared and considers these groups of atoms as rigid bodies. In addition to the functionalities provided by existing tools, RAPIDO can identify structurally equivalent regions also when these consist of fragments that are distant in terms of sequence and separated by other movable domains. Furthermore, RAPIDO takes the variation in the reliability of atomic coordinates into account in the comparison of distances between equivalent atoms by employing weighting-functions based on the refined B-values. The regions identified as equivalent by RAPIDO furnish reliable sets of residues for the superposition of the two structures for subsequent detailed analysis. The RAPIDO server, with related documentation, is available at http://webapps.embl-hamburg.de/rapido.
authors.affiliation: IFOM, the FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Mosca
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Schneider
mesh_terms: D000465:Algorithms; D019731:Carbon-Nitrogen Ligases / Q000737:chemistry; D020407:Internet; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
chemical_list: D019731:Carbon-Nitrogen Ligases; C019791:biotin carboxylase