Featured Resource: PubChem Now Offers 3-D Small Molecule Structures and a New Conformer Viewer (Pc3D)
NCBI’s PubChem now features calculated three-dimensional conformers (3-D conformers) for a large proportion of the PubChem compound database (17 million records, 88%). In addition, conformers are clustered to provide a list of similar 3-D conformers. These similar conformers provide a more relevant and expanded set of compounds with potentially similar biological and pharmacological activity. PubChem also provides a viewer for small molecule conformers and alignments that produces an animated view from displays in the Web service.
The new standalone viewer, Pc3D, is the small-molecule equivalent of the now standard Cn3D viewer for macromolecular structures and provides additional features for visualizing the details of small molecule structures and alignments. These powerful new aspects of PubChem greatly expand the potential of PubChem as a chemical informatics resource for rational biological inhibitor and drug design.
Viewing small molecule conformers and alignments
Figure 1. The PubChem compound summary page for methylphenidate. Clicking the “3D” tab on the “Structure & Quick Link Bar” changes the display to a 3-D conformer. A pop-up menu provides links to display the conformer in the Web-based viewer or the standalone Pc3D viewer.
Figure 1 shows a PubChem Compound record for the stimulant methylphenidate (Compound ID
4158). The small 2-D structural formula is the default graphic on the right-hand-side of the structure summary under the “Structure and Quick Link Bar”. Clicking on the “3D” tab produces the small 3-D graphic shown in the figure. The 3-D viewers are easily launched from this graphic.
Summary
The availability of 3-D conformers and similarities in PubChem greatly expands the utility of the PubChem resource by providing visualization tools and extends the universe of similar compounds. These now include not only simple derivatives but also additional compounds with similar volume, steric and charge features. Analyses using these features will help investigators understand the nature and causes of biological activity and provide new candidates for drug and inhibitor design.
References
1. Fontaine F, Bolton E, Borodina Y, Bryant SH. (2007) Fast 3D shape screening of large chemical databases through alignment-recycling. Chem Cent J. Jun 6;1:12.
2. Borodina YV, Bolton E, Fontaine F, Bryant SH. (2007) Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. J Chem Inf Model. Jul-Aug;47(4):1428-37.
New Databases and Tools
Genome Build
Build 1.1 of the genomes Hydra magnapapillata and Taeniopygia guttata (zebra finch) are available in the Genomes database and on the NCBI Map Viewer. The Map Viewer page is: http://www.ncbi.nlm.nih.gov/mapview/
Bookshelf
The Bookshelf has added four new books: Electrochemical Methods for Neuroscience, Frontiers in Neuroscience, Indwelling Neural Implants: Strategies for Contending with the InVivo Environment, and The National Academies Collection: Reports Funded by National Institutes of Health. The Bookshelf website URL is: www.ncbi.nlm.nih.gov/sites/entrez?db=Books
GenBank News
GenBank release 170.0 is available from the NCBI Web and FTP sites. The current release includes information available as of February 13, 2009. With this release, the new DBLINK linetype is now valid for GenBank sequence records, and it will begin to appear in GenBank Update files, soon after GenBank 170.0 is made available. Release notes are on the on the ftp site: ftp.ncbi.nih.gov/genbank/gbrel.txt
Updates and Enhancements
NCBI News
The NCBI News is now available in PDF format. There is a link for “Printable Copy” in the top right corner of each issue. Clicking that link will allow users to read and print a PDF version of the News.
RefSeq
RefSeq Release 34 is now available via Entrez and FTP. This full release incorporates genomic, transcript, and protein data available as of March 6, 2009. It includes 10,021,870 records from 8,054 different species and strains. The RefSeq website is: www.ncbi.nlm.nih.gov/RefSeq/. The FTP site is: ftp.ncbi.nlm.nih.gov/refseq/release. Changes since the previous release can be found in the release notes on the FTP site.
PubMed
Two new features have been added to the PubMed Abstract Plus Display to enhance discovery within the NCBI databases. Ads now appear in the right-hand discovery column, which provide additional links to related data. One new ad provides a link to the structure database if a structure is reported in the article, and a second ad provides links to PubMed Central articles that have cited the PubMed article being viewed.
Map Viewer
A new feature has been added to the Map Viewer homepage that links directly to a region on a chromosome. Clicking the “R” icon next to an organism name opens a box that provides options for chromosome number, assembly, and coordinate range. This feature links directly to the entered position on the given genome. The Map Viewer website is: www.ncbi.nlm.nih.gov/mapview/.
Exhibits
NCBI will be exhibiting at the American Society for Microbiology’s 190th General Meeting on May 17-21 in Philadelphia, Pennsylvania.
Announce Lists and RSS Feeds
Fifteen topic-specific mailing lists are described on the Announcement List summary page. Announce lists provide email announcements about changes and updates to NCBI resources. www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html
Seven RSS feeds are now available from NCBI including news on PubMed, PubMed Central, NCBI Bookshelf, LinkOut, HomoloGene, UniGene, and NCBI Announce. Please see: www.ncbi.nlm.nih.gov/feed/
Comments and questions about NCBI resources may be sent to NCBI at: info@ncbi.nlm.nih.gov, or by calling 301-496-2475 between the hours of 8:30 a.m. and 5:30 p.m. EST, Monday through Friday.