CAPS-DB
- CAPS-DB CAPS-DB is a structural classification of helix capping motifs or CAPS
compiled from protein structures. Nt and Ct capping motifs have been grouped into structural clusters using a
computational method designed to this purpose. Briefly, caps were structurally clustered by using geometrical descriptors and comparing of the main chain phi/psi angles.
The RMSD (Root Mean Square Deviation) of C-alpha atoms was used to assess the quality of the clusters. Clusters are organized into a fully browsable tree-like hierarchical
model that includes the type of capping (Nt or Ct), geometry and conformation.
PCRPi-DB
- PCRPi-DB is a repository of annotated hot spots in protein
interfaces using PCRPi , a computational method designed to predict critical or hot spot residues in protein
interfaces by combining structural,
evolutionary and energy-based information. Hot spots have been annotated in any protein complexes for which the 3D-structure is known, are deposited
in the PDB databank, and are solved with a crystal resolution better than 3 Ang. PCRPi-DB is weekly
updated.
ArchDB
- ArchDB is a compilation of structural classifications of loops extracted from
protein structures. Currently, ArchDB contains more than 100,000 loops classified into more than 10,000
subclasses. ArchDB have been successfully applied in structure prediction of loops and
functional annotation of proteins. The database provides an easy way to retrieve functional information from
protein structures sharing a common motif, to search motifs found in a given SCOP family, superfamily or fold, search for templates to model
loop structures, and search for functional loops.
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