RCSB PDB Offers Web Services

The RCSB PDB has introduced Web Services to help the software developer community build tools that interact more effectively with PDB data. Instead of storing coordinate files and related data locally, web services provide a way for software tools to interact with the RCSB PDB remotely.

The RCSB PDB's web services were implemented using Axis (http://ws.apache.org/axis/) and include BLAST, FASTA, PubMed, and SNP queries. A complete list of web services and their WSDL description (Web Services Description Language in XML Format) are available.

Web services allow the developer community to build applications that are platform independent and require only a traditional HTTP connection. This is especially useful for developing in environments with relatively tight security constraints. Web services also provide a low-overhead approach to designing workflow applications that integrate remote services. Developers can write efficient and manageable distributed tools without having to worry about low-level communication details. Using web services, programmers can write efficient workflow tools. For example, a developer could write a tool that interoperates between local data, PDB data, and NCBI data.

For general information on web services, please visit http://www.w3.org/2002/ws/.

Automated Downloads of PDB Data

The RCSB PDB FTP site provides coordinate data (in PDB, mmCIF, and PDBML/XML formats) and experimental data. A web interface offers a way to download multiple data files from the archive. Scripts are also available to assist in the automated download of data from the ftp site:

ftp://snapshots.rcsb.org/rsyncSnapshots.sh
Makes a local copy of an annual snapshot or sections of the snapshot. This script is annotated to assist in downloading only sections of the archive. The time required to download the entire archive can be lengthy (18+ hours); however, the time required to download the coordinate data in a single format should be much less. While the amount of time depends upon network speed, our tests show that all of the coordinate files in PDB format from a snapshot can be downloaded in about 2 1/2 hours.

ftp://ftp.rcsb.org/pub/pdb/software/rsyncPDB.sh
Copies the current contents of the entire archive.

ftp://ftp.rcsb.org/pub/pdb/software/getPdbStructures.pl
Copies portions of the archive.

ftp://ftp.rcsb.org/pub/pdb/software/getPdbUpdate.pl
Copies the data from the weekly updates.

Questions and comments about these scripts should be sent to info@rcsb.org.

WEBSITE STATISTICS

Access statistics for www.pdb.org are given below for the second quarter of 2006.

RSS Functionality at the RCSB PDB

An RSS (Really Simple Syndication) feed provides users with a list of newly updated structures as soon as they are available. RSS pushes information that can be read by client software (an RSS reader) that sits on your local computer. Rather than going to look for new PDB entries, they can come to you.

To start, download and install an RSS reader. Depending on your reader, either drag or click on the orange RSS icon from the top of the RCSB PDB home page (located just next to the latest release date) to add the URL for new structures to your RSS reader.

You will now be informed of new structures as they become available. Clicking on the update notice will take you to the list of new structures.

Some examples of RSS readers include:

For more information on RSS see the following: