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PubChem: An Open Repository for Chemical Structure and Biological Activity Information Steve Bryant

PubChem: An Open Repository for Chemical Structure and Biological Activity Information Steve Bryant. The NIH Biowulf Cluster: 10 Years of Scientific Supercomputing February 3, 2009. PubChem Overview … . … NIH “Molecular Libraries” … Basic design / approach

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PubChem: An Open Repository for Chemical Structure and Biological Activity Information Steve Bryant

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  1. PubChem: An Open Repository forChemical Structure andBiological Activity InformationSteve Bryant The NIH Biowulf Cluster: 10 Years of Scientific Supercomputing February 3, 2009

  2. PubChem Overview … … NIH “Molecular Libraries” … Basic design / approach … Current discovery tools / example … Planned discover tools … New discovery tools ?

  3. NIH Molecular Libraries Program … Technology Development Informatics Screening Instrumentation Cheminformatics Research Centers Molecular Libraries Screening Centers Network (MLSCN) Assay Development Chemical Diversity Compound Repository (MLSMR) Predictive ADMET

  4. Hit List Customized Assay Optimization Chemistry Compound Repository Molecular Libraries BioAssays … Peer review Assay Investigator Screen Hit picking, confirmation, secondary screens

  5. Molecular Libraries Components …

  6. MLSCN Created … 2005

  7. MLPCN Created … 2008

  8. PubChem Overview … … NIH “Molecular Libraries” overview … Basic design / approach … Current discovery tools / example … Planned discover tools … New discovery tools ?

  9. PubChem Approach … … “GenBank model” … direct depositions by investigators … highly automated (low database cost) … 25 year precedents in biology … less precedent in chemical biology

  10. Growth In PubChem Contributing Organizations

  11. PubChem Contents … … Contributed substance records … with chemical structure … chemical names and comments … links to contributor web sites … contributed links to other NCBI biomedical databases

  12. Growth In PubChem Substances / Compounds

  13. PubChem Standardization ...

  14. PubChem Standardization ...

  15. PubChem Contents … … Contributed bioassay records … with assay description / protocol … links to tested substances … summary and detailed test results … links to contributor web sites and other NCBI databases

  16. Growth In PubChem BioAssays

  17. Growth In PubChem Tested Substances

  18. PubChem Overview … … NIH “Molecular Libraries” overview … Basic design / approach … Current discovery tools / example … Planned discover tools … New discovery tools ?

  19. PubChem Retrieval System … … Optimize “discoverability” for molecular biologists by integrating PubChem into NCBI’s Entrez / PubMed Search Engine … Chemical structure search … Bioassay result search … Structure-activity tools

  20. NCBI’s Entrez Search Engine ...

  21. Entrez Links and Neighbors ... 2,000,000 users ... 60,000,000 hits ... … per day VAST Structure Similarity Protein 3D Structure Activity Profile Similarity Bioactivity Screens Target Sequence Similarity PubChem Small Molecules Chemical Structure Similarity Term Frequency Statistics PubMed Literature Protein Sequences

  22. PubChem Users per Day

  23. Search for “Shoichet inhibitors” ...

  24. PubMed Article Retrieved ...

  25. Link to PubChem Records ...

  26. “Kaempferol” in PubChem ...

  27. Similar Compounds in PubChem ...

  28. “Quercetin” in PubChem ...

  29. Compare Protein / Ligand Complexes ...

  30. Link to Another Structure ...

  31. Tyrosine Kinase Family Member ...

  32. Links from “Quercetin” to PubMed ...

  33. PubMed Records ...

  34. Links from Quercetin to BioAssays ...

  35. BioAssay records ...

  36. BioAssay where “Active” ...

  37. BioAssay where “Active” ...

  38. BioAssay where “Active” ...

  39. BioAssay where “Active” ...

  40. Entrez Links and Neighbors ... 2,000,000 users ... 60,000,000 hits ... … per day VAST Structure Similarity Protein 3D Structure Activity Profile Similarity Bioactivity Screens Target Sequence Similarity PubChem Small Molecules Chemical Structure Similarity Term Frequency Statistics PubMed Literature Protein Sequences

  41. PubChem Retrieval System … … Optimize “discoverability” for molecular biologists by integrating PubChem into NCBI’s Entrez / PubMed Search Engine … Chemical structure search … Bioassay result search … Exploratory structure-activity tools

  42. Compounds Similar to Quercetin ...

  43. PubChem Bioactivity Analysis ...

  44. PubChem Bioactivity Analysis ...

  45. PubChem Structure-Activity ...

  46. Active Compound Cluster ...

  47. BioAsay Cluster ...

  48. Another BioAssay Cluster ...

  49. PubMed Connection ...

  50. PubChem Structure-Activity ...

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