title: ProML--the protein markup language for specification of protein sequences, structures and families.
abstract: We propose a specification language ProML for protein sequences, structures, and families based on the open XML standard. The language allows for portable, system-independent, machine-parsable and human-readable representation of essential features of proteins. The language is of immediate use for several bioinformatics applications: we discuss clustering of proteins into families and the representation of the specific shared features of the respective clusters. Moreover, we use ProML for specification of data used in fold recognition bench-marks exploiting experimentally derived distance constraints.
authors.affiliation: Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Hanisch
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D011381:Programming Languages; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins