SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Online resources of potential interest to SCOPe users

  • SCOP2 prototype of a new structural classification of proteins

  • Structural alignments for proteins with non-trivial relationships (SISYPHUS)
  • Hidden Markov Model library for SCOP superfamilies (SUPERFAMILY)

  • Structural similarity search of older version of SCOP using SSM (now PDBeFold)
  • Combinatorial Extension (CE) method for structural comparison
  • PALI pairwise and multiple alignments of SCOP and SCOPe families
  • PASS2 automated structural alignments of SCOP superfamilies
  • SUPFAM structure/sequence relationships
  • Stuctural alignment of SCOP sequences (database + server)

  • Sequence similarity search of SCOP using FPS
  • Universal Protein Resource (UniProt)
  • Pfam database of protein families and HMMs
  • Integrated resource for protein families (InterPro)

  • CATH/Gene3D structural and evolutionary classification
  • ECOD evolutionary classification of protein domains
  • Dali structural comparison and FSSP structural classification
  • 3Dee Protein Domain Definitions

  • Protein Data Bank (PDB)
  • Macromolecular Structure Database (EBI)
  • Nucleic Acid Database (NDB)

  • Swiss-Model
  • Macromolecular Motions Database

  • Genome Census
  • Function assignment and metabolic models