June 15, 2011 (Vol. 31, No. 12)
Strong Points: Nice interface with 3-D structures, many ways to search
Weak Points: One tab (InterPreTS) not functional
DID you know that you can easily explore protein domain-domain and domain-motif interactions in all of their 3-D glory? That’s right, you can take your investigation to another dimension with 3DID, a database that combines protein domain interaction data with high-resolution 3-D protein structures. The website allows users to search by domain name, motif name, Pfam access code, or FASTA sequence and view interactions for the protein of interest via a freely rotatable Jmol structure. One can also browse the database. Conveniently, the top ten domains/motifs with the “most distinct interaction partners” are also displayed. (Any guess for the number one domain? Yep, that’s right: V-set. Obviously…) Finally, there is also a third option for exploring the database: one can search for direct interactions or paths between domains or motifs. These folks seem to have thought of everything!