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November 15, 2007 (Vol. 27, No. 20)

PDBBind Database

  • Refined/filtered info
  • Registration required
If there is a thermodynamic principle for “when it rains, it pours,” then I must be experiencing it as I write this up. After looking for useful thermodynamic sites for some time, I come across two in one evening. This one is more limited in scope thermodynamically than ProNIT, focusing mainly on binding affinities of proteins in the Protein Data Bank (PDB). As described on the site, a considerable amount of filtering and funneling of information from PDB data yields a “refined set” of about 1,300 entries (from over 40,000 PDB entries) containing binding affinities for the protein-ligand complex. Access requires registration, but this is free for researchers in academic, governmental, and noncommercial institutions. Results obtained from searches are e-mailed back to the user’s address. While the interface is a bit more cumbersome than the ProNIT database, the refinements of PDBBind may make it worthwhile to many users.
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  • Weak Points
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