Protein Workshop: A Visualization Tool

Protein Workshop is a new molecular viewer available from the RCSB PDB from every structure summary page. Its simple interface lets users quickly and easily select structural elements to change the coloring, labeling, and representation style (ribbons, cylinders, and more). Users can also color specific structural features based on conformation type, hydrophobicity, and residue type.

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 Java 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 the program.

Protein Workshop Tutorial:Click Here

Mbt: http://mbt.sdsc.edu/
JOGL: https://jogl.dev.java.net/

Figures created using Protein Workshop should cite the RCSB PDB and the mbt (J.L. Moreland, A.Gramada, O.V. Buzko, Qing Zhang and P.E. Bourne. The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications. BMC Bioinformatics, 6:21 (2005))

Protein kinase visualized using Protein Workshop. (1atp: Zheng J, Trafny EA, Knighton DR, Xuong NH, Taylor SS, Ten Eyck LF, Sowadski JM. 2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor. Acta Crystallogr D Biol Crystallogr. 1993 49:362-5.)

Advanced Search Tutorial

The majority of simple searches of the RCSB PDB website are performed using the keyword box at the top of each page. More specific and complex searches are possible using the "Advanced Search" that appears at the top of each page. The Advanced Search fully unleashes the power of the RCSB PDB query engine.

The screen shot shows the Advanced Search page. The circled "Quick Feature Guide" launches the Advanced Search tutorial. This short animated and narrated feature requires Flash software.

At the conclusion of the tutorial, which describes the major features of advanced search, the listener has the option to go to a further advanced search help page for full details of using all the features of advanced search. If you have any problems using advanced search, email info@rcsb.org for help. Suggestions for improvements are always welcome.

WEBSITE STATISTICS

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