Revised version LU TP 02-08 November 21, 2002 Testing Similarity Measures with Continuous and Discrete Protein Models Stefan Wallin ∗ Complex Systems Division, Dept. of Theoretical Physics Lund University, S¨olvegatan 14A, SE-223 62 Lund, Sweden Jochen Farwer † Free University of Berlin, Dept. of Biology, Chemistry and Pharmacy, Institute of Chemistry, Takustr. 6, D-14195 Berlin, Germany Ugo Bastolla ‡ Centro de Astrobiolog´ ıa (CSIC-INTA), Ctra. de Ajalvir km. 4, 28850 Torrej´on de Ardoz (Madrid), Spain to appear in Proteins Struct. Funct. Genet. * E-mail:stefan@thep.lu.se † E-mail:farwer@chemie.fu-berlin.de ‡ E-mail:bastollau@inta.es 1