title: PubChem3D: a new resource for scientists.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Bolton
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.forename: Sunghwan
authors.initials: S
authors.lastname: Kim
authors.forename: Lianyi
authors.initials: L
authors.lastname: Han
authors.forename: Siqian
authors.initials: S
authors.lastname: He
authors.forename: Wenyao
authors.initials: W
authors.lastname: Shi
authors.forename: Vahan
authors.initials: V
authors.lastname: Simonyan
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.forename: Paul A
authors.initials: PA
authors.lastname: Thiessen
authors.forename: Jiyao
authors.initials: J
authors.lastname: Wang
authors.forename: Bo
authors.initials: B
authors.lastname: Yu
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant