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PubChem:An Information Resource
Linking Chemistry and Biology
Evan E. Bolton, Ph.D.
ACS National Meeting
San Francisco, CA
September 10, 2006
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ChemicalDiversity
Technology Development Screening
Instrumentation
AssayDevelopment
PredictiveADMET
Compound Repository(MLSMR)
Molecular LibrariesScreening Centers
Network (MLSCN)
Informatics
CheminformaticsResearch Centers
The Molecular Libraries Roadmap:An Integrated Initiative
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… Archive molecular structure and bioassay data from the Molecular
Libraries Screening Center Network
… Provide search, retrieval and data analysis tools to optimize utility of these
results
PubChem Goals …
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… Further optimize research utility by including other public sources of chemical structure and bioactivity
information
… and by integration with other NIH Biomedical information resources
whenever possible
PubChem Goals …
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… An on-line resource providing comprehensive information on the
biological activities of small molecules
… Accessible to molecular biologists
… Useful to computational / medicinal chemists and other specialists
PubChem Goals …
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… “GenBank model”
… direct depositions by investigators
… highly automated (low database cost)
… 25 year precedents in biology
… less precedent in chemistry
PubChem Approach …
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… Contributed substance records
… with chemical structure
… chemical names and comments
… links to contributor web sites
… contributed links to other NCBI biomedical databases
PubChem Contents …
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… 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
PubChem Contents …
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PubChem Contents ...
… 279 Bioassays Contributed
… 691,387 Bioassay Test Results
… 12,793,312 Substances Contributed
… 7,995,947 Unique Compound Structures
… 54 Depositing Organizations
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Growth in PubChem Substances
0
2000000
4000000
6000000
8000000
10000000
12000000
14000000
May-05
Jun-05
Jul-05
Aug-05
Sep-05
Oct-05
Nov-05
Dec-05
Jan-06
Feb-06
Mar-06
Apr-06
May-06
Jun-06
Jul-06
Date
Cou
nt
CompoundSubstance
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Growth in PubChem BioAssays
170
190
210
230
250
270
290
Aug-05 Sep-05 Oct-05 Nov-05 Dec-05 Jan-06 Feb-06 Mar-06 Apr-06 May-06 Jun-06 Jul-06
Date
Bio
Ass
ay C
ount
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0
5000
10000
15000
20000
250009/
23/2
004
11/2
3/20
04
1/23
/200
5
3/23
/200
5
5/23
/200
5
7/23
/200
5
9/23
/200
5
11/2
3/20
05
1/23
/200
6
3/23
/200
6
Growth in PubChem Users per Day
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… 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
PubChem Retrieval System …
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NCBI’s Entrez Search Engine ...
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Entrez Links and Neighbors ...
Protein Sequences
Protein3D Structure
ActivityProfile
Similarity *
PubChemSmall
Molecules
PubMedLiterature
BioactivityScreens
VAST StructureSimilarity
TermFrequencyStatistics
ChemicalStructureSimilarity
1,500,000 users ...50,000,000 hits ...
… per day
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Search for “Kaempferol” ...
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Compounds in PubChem ...
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Compound in PubChem ...
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Link to Contributor Site ...
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Link to Protein 3D Structures ...
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Link to Protein 3D Structure ...
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Similar Compounds in PubChem ...
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A Similar Compound ...
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Link to Protein 3D Structures ...
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Compare Protein / Ligand Complexes ...
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Link to Contributor Site ...
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Link to Another Structure ...
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Link to Protein Classification ...
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View Protein Family Alignment ...
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Links from Compounds to PubMed ...
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Links from Compounds to PubMed ...
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Link to BioAssays where “Active” ...
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A BioAssay where “Active” ...
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A BioAssay where “Active” ...
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A BioAssay where “Active” ...
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Entrez Links and Neighbors ...
Protein Sequences
Protein3D Structure
ActivityProfile
Similarity *
PubChemSmall
Molecules
PubMedLiterature
BioactivityScreens
VAST StructureSimilarity
TermFrequencyStatistics
ChemicalStructureSimilarity
1,500,000 users ...50,000,000 hits ...
… per day
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… 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
PubChem Retrieval System …
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Structure Search Tool ...
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With Sketcher and Search Options ...
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Search Results Pass to Entrez ...
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BioAssay Search Tool ...
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Select Experimental Results ...
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For Selected PubChem Compounds ...
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PubChem BioAssay Results ...
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Quercetin Structure-Activity ...
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BioAssay Summary Tool ...
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BioAssay Summary Tool ...
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ACE Inhibitors Structure-Activity ...
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Structure Clustering Tool ...
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Members of One Structure Cluster ...
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With Confirmed ACE Inhibitor ...
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MKP-1 Inhibitors Structure-Activity ...
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Actives for MKP-1 BioAssay ...
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Structurally Diverse ...
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Active in other BioAssays ...
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Expand to Similar Structures ...
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Structure Clustering Tool ...
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One Structure Cluster ...
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Mostly Active in Related BioAssays ...
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Though not the Expected Mechanism ...
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Other Analysis Tools Coming ...
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http://pubchem.ncbi.nlm.nih.govSteve Bryant
Yulia BorodinaJie Chen
Svetlana DrachevaFabien Fontaine
Lewis GeerJane He
Siqian HeWolf-Dietrich Ihlenfeldt
Karen KarapetianVahan SimonyanBen Shoemaker
Wenyao ShiTugba Suzek
Paul ThiessenValery Tkachenko
Jiyao WangYanli WangJewen XiaoJian Zhang