Structures stored within PubChem Compound are cross-referenced and pre-clustered by identity and similarity group concepts [2].
Also, unlike Orac, which can make any structure, Monolith resembles the Protein Rezzing Toolkit in that it is limited to structures stored in PDB format.
Nevertheless, nearly 30%% of the protein structures stored in the Protein Data Bank (PDB [36], do not provide information about the exact location of their ligand binding sites [37].
The CREDO structural interactomics database [13] contains the interatomic interactions between all macro- and small molecules found in three-dimensional structures stored in the Protein Data Bank (PDB) [14].
The most interesting features, at the post-processing stage, is that chemOCR uses a graph-matching algorithm to select the best-matching chemical structure fragment against sub-graphs of chemical structures stored in a database.
To efficiently investigate these rich solution neighborhoods, tentative local search move are statically encoded by data structures stored in Fibonacci Heaps which are special priority queue structures offering fast minimum retrieval, insertion and deletion capabilities.
Nevertheless, many of the protein structures stored in public databases do not provide information about the location and characteristics of ligand binding sites and/or other important 3D patterns such as allosteric sites, enzyme-cofactor interaction motifs, etc.
Towards that end, we created the RNAJunction database, which is a repository of RNA junctions, i.e. internal, multi-branch and kissing loops with emanating stem stubs, extracted from the larger RNA structures stored in the PDB database.
However, despite their enormous utility, structures stored at the PDB provide only a partial view of 3D structure.
