Sunghwan Kim - PubChem3D: A new resource for scientists

Version 5

      Publication Details (including relevant citation   information):

      E.E. Bolton, J. Chen, S. Kim, L. Han, S. He, W.   Shi, V. Simonyan, Y. Sun, P. Thiessen, J. Wang, B. Yu, and S.H.   Bryant;

      Journal of Cheminformatics, 2011,   3, 32.





      PubChem is an open repository for small molecules and their   experimental biological activity. PubChem integrates and provides   search, retrieval, visualization, analysis, and programmatic   access tools in an effort to maximize the utility of contributed   information. There are many diverse chemical structures with   similar biological efficacies against targets available in   PubChem that are difficult to interrelate using traditional 2-D   similarity methods. A new layer called PubChem3D is added to   PubChem to assist in this analysis.


      PubChem generates a 3-D conformer model description for 92.3% of   all records in the PubChem Compound database (when considering   the parent compound of salts). Each of these conformer models is   sampled to remove redundancy, guaranteeing a minimum   (non-hydrogen atom pair-wise) RMSD between conformers. A diverse   conformer ordering gives a maximal description of the   conformational diversity of a molecule when only a subset of   available conformers is used. A pre-computed search per compound   record gives immediate access to a set of 3-D similar compounds   (called "Similar Conformers") in PubChem and their respective   superpositions. Systematic augmentation of PubChem resources to   include a 3-D layer provides users with new capabilities to   search, subset, visualize, analyze, and download data. A series   of retrospective studies help to demonstrate important   connections between chemical structures and their biological   function that are not obvious using 2-D similarity but are   readily apparent by 3-D similarity.


      The addition of PubChem3D to the existing contents of PubChem is   a considerable achievement, given the scope, scale, and the fact   that the resource is publicly accessible and free. With the   ability to uncover latent structure-activity relationships of   chemical structures, while complementing 2-D similarity analysis   approaches, PubChem3D represents a new resource for scientists to   exploit when exploring the biological annotations in PubChem.


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