PubChem News

IBM contributed structures in PubChem

2011-12-08T17:18:00-05:00

More than 2.5 million structures from the IBM BAO (Business Analytics and Optimization) strategic IP insight platform (SIIP) are now available in PubChem, aggregating data from millions of patents and from the scientific literature through the year 2000. The chemical substances were extracted from the textual content, images, and symbols in patents and literature. The PubChem records link to the IBM web site, where files that list the patent numbers and PubMed IDs for each substance can be downloaded. See more related news...

PubChem compound and substance summary updated

2011-10-05T10:22:16-05:00

PubChem updated the compound and substance summary pages to load faster, to include dramatically expanded biomedical annotation, and to give an updated look and feel. For example, the PubChem Compound summary page for aspirin (CID 2244).

PubChem3D added as a new layer

2011-10-03T14:20:56-05:00

A new layer called PubChem3D is added to PubChem to assist with interrelating diverse chemical structures with similar biological efficacies against targets. As a part of this, PubChem computes a 3-D conformer model description for records in the PubChem Compound database when possible (92% of all records when considering the parent compound of salts). 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. For additional information, please visit the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d.

PubChem growth in 2011

2011-08-12T15:00:51-05:00

PubChem in 2011 - Growth Continues

PubChem's information content continues to increase. As of August, 2011, deposited substance records have reached 85 million, representing to over 30 million chemically unique compounds. Deposited bioassay records have reached 500 thousand, representing over 130 million experimental bioactivity results. New substance and bioassay records continue to be deposited, and the PubChem team expects that the steady growth in content and usage seen over the past 7 years will continue.

AmicBase deposited substances in PubChem

2011-08-10T11:27:28-05:00

Structures from AmicBase are now available in PubChem.

PubChem's new data retrieving tool released

2011-06-08T15:27:45-05:00

PubChem is now providing an enhanced bioactivity analysis tool for retrieving bioassay data for a chemical. The tool can be accessed at http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?cid=myCID for a given CID or http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgisid=mySID for a given SID.
E.g. For CID 2244, the link is: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?cid=2244

To find out a CID associated with bioactivity data, you may follow the URL at http://www.ncbi.nlm.nih.gov/pccompound?term=pccompound_pcassay_active[filt]. Similarly, to find out a SID associated with bioactivity data, you may follow the URL at http://www.ncbi.nlm.nih.gov/pcsubstance?term=pcsustance_pcassay_active[filt]. You may also go to the advanced search page for PubChem Compound database or Substance database, and followed by making a choice in the "BioAssays" section and clicking the "Go" button.

PubChem Identifier Exchange Service released

2011-05-27T19:46:38-05:00

PubChem released the Identifier Exchange Service. For more information, click here.

The BioAssay data specification updated

2011-05-23T17:05:32-05:00

The BioAssay data specification has been updated. The changes include:

New units in PC-ResultType to facilitate DMPK data submission.
A new element "type" in PC-AnnotatedXRef to record primary citation to advertise primary publications of the depositors and the bioassay results.
A new element "type" in PC-AssayDRAttr to record experimental vs. calculated dose-response data points.

Please review the update at ftp://ftp.ncbi.nlm.nih.gov/pubchem/data_spec.

PubChem released two new data analysis tools

2011-04-11T09:46:08-05:00

PubChem released two new data analysis tools for the bioassay services - Target and Compound/Substance views for the BioActivity Analysis service. These new tools together with the original bioassay view component will allow users to explore bioactivity data from molecular target, chemical structure, and biological experiment perspectives. For more information, see the related section in the help page.

A new depositor from Calicut University

2011-03-17T22:01:02-05:00

Structures from Immunology Lab, Department of Biotechnology, Calicut University are now available in PubChem.

AKos deposited substances in PubChem

2011-03-15T18:47:53-05:00

Structures from AKos are now available in PubChem.

DRSC deposited RNAi data in PubChem

2011-02-22T12:07:45-05:00

RNAi screening data and substances from the Drosophila RNAi Screening Center (DRSC) are now available in PubChem.

Substance vendor - ABI Chem in PubChem

2011-02-22T12:00:24-05:00

Structures from ABI Chem are now available in PubChem.

Two new depositors in PubChem

2011-02-07T08:36:55-05:00

Structures from Alsachim are now available in PubChem.

Structures and bioassay data from UCLA Molecular Screening Shared Resource are now available in PubChem.

ChEMBL assays updated

2011-01-19T10:30:13-05:00

All ChEMBL assays have been updated and now point to substances deposited by ChEMBL requested by ChEMBL and ChEBI.

PubChem BioAssay data spec updated

2011-01-13T09:59:05-05:00

The PubChem BioAssay ASN.1/XML data specification has been updated to include new types of target data under PC-AssayTargetInfo and PC-ResultType. For more details, please refer to ftp://ftp.ncbi.nlm.nih.gov/pubchem/data_spec.

Abbott deposited substances and bioassay data in PubChem

2011-01-11T14:14:42-05:00

Structures and bioassay data from Abbott are now available in PubChem.

AAA Chemistry deposited substances in PubChem

2010-12-20T16:06:32-05:00

Structures from AAA Chemistry are now available in PubChem.

Kingston Chemistry deposited substances in PubChem

2010-12-16T12:40:39-05:00

Structures from Kingston Chemistry are now available in PubChem.

Substance vendor Avanti Polar Lipids in PubChem

2010-11-10T12:10:10-05:00

Structures from Avanti Polar Lipids are now available in PubChem.

Excenen PharmaTech deposited substances in PubChem

2010-11-01T12:57:09-05:00

Structures from Excenen PharmaTech are now available in PubChem.

Selleck Chemicals deposited substances in PubChem

2010-10-29T10:37:39-05:00

Structures from Selleck Chemicals are now available in PubChem.

Zancheng deposited structures in PubChem

2010-10-08T12:54:41-05:00

Structures from Zancheng Functional Chemicals are now available in PubChem.

The PubChem BioAssay FTP updated

2010-09-03T14:10:25-05:00

To expedite the download speed for growing number of assays in the PubChem Bioassays FTP site, we have introduced several changes that may impact all of the BioAssay FTP users.

Data and description files are now partitioned and compressed as "zip" format. Each compressed zip file contains a directory with a list of BioAssay files according to the range of AID(BioAssay ID), the directory named as the AID range, and each individual data filename prefixed by the AID. For example, the file "0000001_0001000.zip" contains the compressed zip archive directory which contains individual Bioassay files. Each Bioassay file contains an AID record within the range of 1 through 1,000.
The files were partitioned according to a fixed AID range of 1000.
The zip file format has been natively supported on Windows, Mac OS X, Linux, Unix and other systems. There are also a number of ZIP tools and libraries available and free for your programming environments.

ICCB at Harvard deposited bioassay data in PubChem

2010-09-03T14:08:02-05:00

Bioassay data from the ICCB-Longwood/NSRB Screening Facility, Harvard Medical School are now available in PubChem.

The PubChem data specification updated

2010-09-03T14:05:10-05:00

1. ASN1/XML data specification for PubChem Substance has been modified to include XRef choices for cross-link to NCBI GEO database.

2. ASN1/XML data specification for PubChem BioAssay has been modified to Include "categorized-comment" field under PC-AssayDescription.

For more details, please refer to ftp://ftp.ncbi.nlm.nih.gov/pubchem/data_spec

Finley and King Labs deposited substances and data in PubChem

2010-07-12T10:48:03-05:00

Structures and bioassay data from Finley and King Labs, Harvard Medical School are now available in PubChem.

Substance vendor, Annker Organics, in PubChem

2010-06-30T17:00:46-05:00

Structures from Annker Organics are now available in PubChem.

Tractus deposited structures in PubChem

2010-06-21T13:44:08-05:00

Structures from Tractus are now available in PubChem.

Ennopharm in PubChem

2010-06-07T11:21:25-05:00

Structures from Ennopharm are now available in PubChem.

iThemba Pharmaceuticals in PubChem

2010-06-04T09:45:49-05:00

Structures from iThemba Pharmaceuticals are now available in PubChem.

ChEMBL deposited bioassay data in PubChem

2010-05-29T06:39:05-05:00

Bioassay data from ChEMBL are now available in PubChem.

Jamson Pharmachem deposited substances in PubChem

2010-05-28T10:00:55-05:00

Structures from Jamson Pharmachem Technology are now available in PubChem.

Amatye deposited structures in PubChem

2010-05-24T11:02:21-05:00

Structures from Amatye are now available in PubChem.

GSK deposited substances and screening data in PubChem

2010-05-20T17:27:02-05:00

Structures and bioassay screening data from the GlaxoSmithKline (GSK) are now available in PubChem. More news can be found here.

Circadian Research at UCSD deposited structures and screening data in PubChem

2010-04-27T13:57:16-05:00

Structures and small molecule screening data from the Circadian Research, Kay Laboratory, University of California at San Diego (UCSD) are now available in PubChem.

3 New substance depositors in PubChem

2010-04-21T17:13:22-05:00

Structures from the Golm Metabolome Database (GMD), Max Planck Institute of Molecular Plant Physiology are now available in PubChem.

Structures from the Nitric Oxide Research, National Cancer Institute (NCI) are now available in PubChem.

Structures from the Creasyn Finechem are now available in PubChem.

ICCB-Longwood of Harvard Medical School deposited structures in PubChem

2010-04-13T21:28:44-05:00

Structures from the ICCB-Longwood/NSRB Screening Facility, Harvard Medical School are now available in PubChem.

Nature Communications deposited structures in PubChem

2010-04-13T21:27:06-05:00

Structures from the Nature Communications are now available in PubChem.

Tokyo Chemical Industry Deposited Structures

2010-03-05T08:32:49-05:00

Structures from TCI (Tokyo Chemical Industry) are now available in PubChem.

Molport deposited structures

2010-02-19T11:50:10-05:00

Structures from the molport are now available in PubChem.

MIC Scientific deposited structures in PubChem

2009-12-15T11:09:36-05:00

Structures from MIC Scientific are now available in PubChem.

ChEBI release 62 in PubChem

2009-11-23T14:09:25-05:00

Structures from ChEBI are now updated with ChEBI release 62.

Deposition Gateway Upgrade

2009-11-18T17:00:16-05:00

Notice: Upcoming Database Upgrade
The PubChem Deposition Gateway will be unavailable this coming Monday (2009-11-23) from 8:00 AM EST to 2:00 PM EST, due to a required database server upgrade. The actual downtime may be shorter than this window, but it should not exceed it. Please contact NCBI with concerns: info@ncbi.nlm.nih.gov.

Upcoming Systems Maintenance

2009-11-13T10:47:43-05:00

Notice: Upcoming Systems Maintenance
PubChem may experience a partial outage of services this weekend, beginning Friday (2009-11-13) at 3:00 PM EST through Saturday (2009-11-14) at 8:00 PM EST, due to upgrades to the power grid at NCBI. During this time, most PubChem services will be operational but may be intermittently slow. The PubChem Deposition Gateway will be unavailable. Please contact NCBI with concerns: info@ncbi.nlm.nih.gov.

PubChem Entrez added "Selected Records" panel

2009-10-30T15:11:47-05:00

PubChem Entrez displays now include a "Selected Records" panel to help users discover informative annotations and subsets among search results. For example, following a keyword search of PubChem Compound for "aspirin", the "Selected Compounds" panel includes a line saying "Protein 3D Structures, Compound Count: 4." This indicates that 4 of the 85 compound records retrieved by the "aspirin" search were derived from Protein 3D structures. Clicking on "4" shows which 4 out of the 85 compounds were observed binding to proteins. Clicking on "Protein 3D Structures" shows the 20 experimental protein 3D structures observed to bind these compounds.

Ganolix deposited structures

2009-10-30T13:06:11-05:00

Structures from the Ganolix are now available in PubChem.

University of Kansas Specialized Chemistry Center deposited substances in PubChem

2009-09-30T11:27:24-05:00

Structures from the Molecular Libraries Program, University of Kansas Specialized Chemistry Center are now available in PubChem.

siRNA screen data from GNF in PubChem

2009-09-17T16:53:03-05:00

A genome-wide siRNA screen for modifiers of the circadian clock in human cells from the Genomics Institute of the Novartis Research Foundation (GNF) is now available in PubChem.

Biological Magnetic Resonance Data Bank Deposited Structures in PubChem

2009-09-02T13:36:39-05:00

Structures from Biological Magnetic Resonance Data Bank (BMRB) are now available in PubChem.

Tyger Scientific and PennChem-GAM deposited structures in PubChem

2009-08-05T11:30:24-05:00

Structures from Tyger Scientific are now available in PubChem.

Structures from PennChem-GAM are now available in PubChem.

Substance vendor IS Chemical Technology in PubChem

2009-06-30T14:24:40-05:00

Structures from IS Chemical Technology are now available in PubChem.

PDBbind data in PubChem

2009-06-12T10:02:50-05:00

Protein-ligand binding affinity data from the PDBbind database have now been deposited into PubChem BioAssay database by the Shanghai Institute of Organic Chemistry.

PubChem - One of the Best Free Reference Web Sites 2009

2009-06-12T06:58:07-05:00

The ALA (American Library Association) selected PubChem as one of the Best Free Reference Web Sites 2009.

ZINC updated in PubChem

2009-06-09T09:51:53-05:00

Structures from ZINC are updated in PubChem.

Vitas-M deposited structures in PubChem

2009-06-04T05:50:14-05:00

Structures from Vitas-M Laboratory are now available in PubChem.

Two Substance Vendors in PubChem

2009-05-21T07:56:38-05:00

Structures from Shanghai Sinofluoro Scientific Company are now available in PubChem.

Structures from Alinda Chemical are now available in PubChem.

Max Planck Institute of Molecular Physiology deposited structures and bioassay data in PubChem

2009-04-24T10:16:18-05:00

Structures and small molecule screening data from Chemical Biology Department, Max Planck Institute of Molecular Physiology are now available in PubChem.

Novo|seek deposited structures in PubChem

2009-04-02T15:50:39-05:00

Structures from novo|seek are now available in PubChem. Novo|seek is a search engine for biomedical literature in Medline and US Grants.

March 30, 2009

2009-03-30T13:56:06-05:00

Small molecule screening data from Johns Hopkins Ion Channel Center are now available in PubChem.

Small molecule screening data from Broad Institute are now available in PubChem.

Structures and small molecule screening data from NINDS Approved Drug Screening Program are now available in PubChem.

Small molecule screening data from Southern Research Specialized Biocontainment Screening Center are now available in PubChem.

Substances and RNAi screening data from RNAi Global Initiative / Thermo Scientific Dharmacon RNAi Technologies are now available in PubChem.

February 25, 2009

2009-02-25T10:52:05-05:00

Structures from Nature Chemistry are now available in PubChem.

February 13, 2009

2009-02-13T11:02:49-05:00

Structures from Thermo Scientific Dharmacon RNAi Technologies are now available in PubChem.

February 3,2009

2009-02-03T20:40:03-05:00

PubChem3D is released consisting of a single theoretical 3D conformer per compound record and includes a new similarity relationship (Similar Conformers).

XLogP is now updated to version 3.0 of the algorithm. InChI and InChIKey are now updated to use the version 1.0.2 standard.

November 28, 2008

2008-11-28T09:09:48-05:00

Structures from Vanderbilt University Medical Center are now available in PubChem.

November 26, 2008

2008-11-26T06:56:20-05:00

BioAssay data, Kinase Inhibitor Selectivity Profiling Assay, from Ambit Biosciences are now available in PubChem.

November 20, 2008

2008-11-20T07:24:23-05:00

The PubChem Score Matrix Service, through which one can download similarity scores for selected lists of CIDs, is now released.

November 7, 2008

2008-11-07T17:04:57-05:00

BioAssay data from The International Union of Pharmacology (IUPHAR-DB) are now available in PubChem.

November 5, 2008

2008-11-05T10:56:03-05:00

Structures from EMD Biosciences are now available in PubChem.

October 27, 2008

2008-10-27T09:22:54-05:00

Structures from ChemSynthesis are now available in PubChem.

October 20, 2008

2008-10-20T15:48:11-05:00

Structures from PENN-ABS are now available in PubChem.

Structures from IUPHAR-DB are now available in PubChem.

Structures from True PharmaChem are now available in PubChem.

September 29, 2008

2008-09-29T12:23:25-05:00

Structures from Comparative Toxicogenomics Database are now available in PubChem.

Structures from HDH Pharma are now available in PubChem.

Structures from Johns Hopkins Ion Channel Center are now available in PubChem.

Structures from Biosynth are now available in PubChem.

September 18, 2008

2008-09-18T13:39:10-05:00

PubChem PUG SOAP is officially released.

September 18, 2008

2008-09-18T13:38:54-05:00

RSS and Atom feed are available for PubChem announcements.

September 11, 2008

2008-09-11T14:39:32-05:00

Structures from MP Organic & Rare Chemicals are now available in PubChem.

September 10, 2008

2008-09-10T14:39:28-05:00

Structures from NextBio are now available in PubChem.

September 8, 2008

2008-09-08T14:39:25-05:00

Structures from Isoprenoids are now available in PubChem.

August 15, 2008

2008-08-15T14:43:00-05:00

Structures from Ambit Biosciences are now available in PubChem.

Structures from Paul Baures are now available in PubChem.

July 15, 2008

2008-07-15T14:39:07-05:00

Structures from LeadScope are now updated in PubChem.

July 1, 2008

2008-07-01T14:39:16-05:00

Structures from the Hangzhou Trylead Chemical Technology are now available in PubChem.