3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities

Proteins. 2010 Jul;78(9):2101-13. doi: 10.1002/prot.22725.


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.

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / classification
  • Bacterial Proteins / genetics
  • Computational Biology / methods*
  • Drug Design
  • Enzyme Stability
  • Humans
  • Models, Molecular
  • Molecular Diagnostic Techniques
  • Protein Binding
  • Protein Engineering / methods*
  • Proteins / chemistry*
  • Proteins / classification
  • Proteins / genetics
  • Sequence Alignment
  • Sequence Analysis, Protein*
  • Substrate Specificity


  • Bacterial Proteins
  • Proteins