A method for simultaneous alignment of multiple protein structures

By Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson. Proteins: Structure, Function, and Bioinformatics, 2004

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Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners (2008, methodology): “The program MultiProt [156] was used to gen-”
The Structure, Stability and Pheromone Binding of the Male Mouse Protein Sex Pheromone Darcin (2014, methodology): “In addition comparative analysis of the MUP family employed PROMALS3D [42,43] for secondary structure driven sequence alignment and Multiprot [44] for homologous structure alignment.”
Template-based structure modeling of protein-protein interactions (2013, methodology): “In PRISM [23,46], for instance, a non-redundant interface library is used in association with the structural alignment program MultiProt [36] which is capable of aligning segments in a sequence order independent fashion.”
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008, methodology): “Matt and Mustang both do qualitatively better at all discrimination tasks than either MultiProt or FlexProt.”