New Website Features
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The Ligand Hits tab from a search for 'protein kinase'
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The Ligand Summary page offers summary information, downloads (definitions and coordinates), and interactive and static views. HEM is shown here.
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A look in Ligand Explorer at a hydrophobic binding pocket for ATP in entry 1ATP. To access Ligand Explorer, click the 'View' button under 'Ligand Interaction' on the Structure Summary page.
Many enhancements were made for data query and reporting during this quarter.
- Improved Access to Ligand Data
The PDB chemical components dictionary (formerly the HET dictionary) has been remediated to better describe the components that interact with macromolecular structures. This new dictionary has been incorporated with the RCSB PDB database.
Options available after a search now includes a tab called 'Ligand Hits'. This page lists the ligands known to interact with the structures that match the query.
For example, a search for 'protein kinase' returns 2051 structures and 678 ligands. From the 'Ligand Hits' page, users can find all of the structures that contain that ligand or access information from the 'Ligand Summary' page. This page offers summary information, downloads (definitions and coordinates), and interactive and static views.
- Ligand Explorer Tool for Viewing Protein-Ligand Interactions
Ligand Explorer is a Java-based program accessible from each Structure Summary page. Features include the ability to highlight ligand interactions based on conventional and user-defined thresholds and a 'contact map' that shows the details of each interaction.
Support pages for Ligand Explorer are available.
- Access to Single Nucleotide Polymorphism (SNP), Pfam, and more
SNP information is now accessible from the structure summary pages. Over 4000 PDB structures are linked to SNP information from the SNP database. This information is accessible from each entry's 'Biology and Chemistry Report' tab.
The Pfam database contains multiple alignments of protein domains. With each release of the Pfam data, files mapping Pfam domains to PDB structures are made available on the Pfam FTP site. This mapping is loaded into our database and the Pfam domain information for a protein structure is displayed on an entry's Structure Summary page and Biology and Chemistry Report, when available.
The 'External Links' option provides further information about the structure under study, such as biochemical pathway information, stereochemistry and ligand binding data. When looking at an entry's structure summary, the external links page is accessible from the left-hand menu.
SNP: http://www.ncbi.nlm.nih.gov/projects/SNP/
Pfam: http://www.sanger.ac.uk/Software/Pfam/
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The MeSH browser
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Some of the many Advanced Search options
- New Advanced Search Options
Simple searches of the RCSB PDB website can be performed using the keyword box at the top of each page. The "Advanced Search" feature makes more specific and complex searching possible.
New possible queries include:
- Keyword Searching: These options can be used to search with keywords, phrases or a series of keywords.
Advanced Keyword Search: This option can be used to search for keywords in the full text or in the author name. If you enter a phrase, you must place it in quotes otherwise it will be interpreted as a series of keywords. Advanced keyword search supports the lucene syntax for sophisticated string searching.
PubMed: Searches PubMed titles and abstracts for an entry's primary citation (if it exists).
Medical Subject Headings (MeSH): Searches for structures associated with particular MeSH terms from the National Library of Medicine (NLM). This option launches the MeSH Browser, which lets users either browse through the MeSH hierarchical tree or search the tree with keywords.
- Author Assigned: Looks for structures based upon keywords used by the depositor.
Advanced Search Tutorial:
http://www.pdb.org/pdb/tutorials/advancedSearch.html
Advanced Search Help :
http://www.pdb.org/robohelp/advancedsearch/intro.htm
- New Help Features
A new set of Flash Tutorials are available, modeled on the popular guides on how to use the RCSB PDB site overall and how to use the Advanced Search.
Tutorials are now available for the
MeSH Browser,
Protein Workshop,
KiNG,
Jmol, and
general
navigation. They are accessible from the left-hand menu under "Site Tutorials".
Quick Tips are another resource for learning new ways of exploring the RCSB PDB website. These tips offer hints and quick links to get started. To view them, click on the "Show Quick Tips" in the left-hand menu. Clicking on the arrow button will scroll through these hints, and clicking on the X will close the box.
Please write to info@rcsb.org with any questions or comments about these new features.
RCSB PDB Focus: Saving Protein Workshop "States" for Future Visualization Sessions
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A section of MHC as viewed in Protein Workshop. PDB ID: 1hsa. D.R. Madden, J.C. Gorga, J.L. Strominger, D.C. Wiley. (1992) The three-dimensional structure of HLA-B27 at 2.1 Angstrom resolution suggests a general mechanism for tight peptide binding to MHC. Cell 70:1035-1048.
RCSB PDB Focus: Saving Protein Workshop "States" for Future Visualization Sessions
Protein Workshop is a molecular viewer accessible from every PDB entry's Structure Summary page. Its simple interface lets users quickly and easily select structural elements and change the coloring, labeling, and representation style (ribbons, cylinders, and more). Users can also color specific structural features such as conformation type and hydrophobicity.
Protein Workshop is an excellent tool for generating high-resolution images in JPG, BMP, TIFF, WBMP, and PNG formats. A tutorial for creating these images is available.
This tool offers a way to save the "state" of a Protein Workshop session. Users can rotate and zoom a structure to a particular orientation and then capture this view for later use. To save a state, enter a title next to the "Capture current viewer state" from the Options menu, and then select the adjacent button. The name of this state will be listed in the box below. The view of the molecule can then be changed around, but users can always go back to saved states by clicking on the state's name.
These states can be saved in a XML file for later use by selecting the state and clicking the "Export selected state" button. States can be restored from a file by clicking the "Import state" button.
This tool uses the Molecular Biology Toolkit (mbt) and JOGL technology, and requires no installation other than the most recent version of Java. A tutorial is provided to guide users in using Protein Workshop.
Time-stamped Copies of PDB Archive Available via FTP
A time-stamped snapshot of the PDB archive as of January 2, 2007 has been added alongside time-stamped copies of the archive from January 2006 and 2005 at ftp://snapshots.rcsb.org/. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.
The directory 20070102 includes the 40,933 experimentally-determined coordinate files that were current (i.e., not obsolete) as of January 2, 2007. Coordinate data are available in PDB, mmCIF, and XML formats. The date and time stamp of each file indicates the last time the file was modified.
Scripts are available to automatically download data:
WEBSITE STATISTICS
Access statistics for the first quarter of 2007 are given below for the
RCSB PDB website at www.pdb.org.
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