title: 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.
abstract: Ten years of experience with molecular class-specific information systems (MCSIS) such as with the hand-curated G protein-coupled receptor database (GPCRDB) or the semiautomatically generated nuclear receptor database has made clear that a wide variety of questions can be answered when protein-related data from many different origins can be flexibly combined. MCSISes revolve around a multiple sequence alignment (MSA) that includes "all" available sequences from the entire superfamily, and it has been shown at many occasions that the quality of these alignments is the most crucial aspect of the MCSIS approach. We describe here a system called 3DM that can automatically build an entire MCSIS. 3DM bases the MSA on a multiple structure alignment, which implies that the availability of a large number of superfamily members with a known three-dimensional structure is a requirement for 3DM to succeed well. Thirteen MCSISes were constructed and placed on the Internet for examination. These systems have been instrumental in a large series of research projects related to enzyme activity or the understanding and engineering of specificity, protein stability engineering, DNA-diagnostics, drug design, and so forth.
authors.affiliation: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, 6525 GA Nijmegen, The Netherlands.
authors.forename: Remko K
authors.initials: RK
authors.lastname: Kuipers
authors.forename: Henk-Jan
authors.initials: HJ
authors.lastname: Joosten
authors.forename: Willem J H
authors.initials: WJ
authors.lastname: van Berkel
authors.forename: Nicole G H
authors.initials: NG
authors.lastname: Leferink
authors.forename: Erik
authors.initials: E
authors.lastname: Rooijen
authors.forename: Erik
authors.initials: E
authors.lastname: Ittmann
authors.forename: Frank
authors.initials: F
authors.lastname: van Zimmeren
authors.forename: Helge
authors.initials: H
authors.lastname: Jochens
authors.forename: Uwe
authors.initials: U
authors.lastname: Bornscheuer
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend
authors.forename: Vitor A P Martins
authors.initials: VA
authors.lastname: dos Santos
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Schaap
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D004795:Enzyme Stability; D006801:Humans; D008958:Models, Molecular; D025202:Molecular Diagnostic Techniques; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D011506:Proteins