International Protein Data Bank Enhanced by Computer Browser

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Access to the Protein Data Bank (PDB), a major international resource archiving the three-dimensional structures of thousands of proteins, nucleic acids and other biological macromolecules, has been greatly enhanced by a computer utility developed through a collaboration of Weizmann Institute and Brookhaven National Laboratory researchers. The new browser, described in a recent issue of Nature, facilitates database usage by making index listings and ad-hoc search protocols far more user-friendly.

Data on crystal structures -- important for understanding protein function, engineering novel proteins and designing new drugs -- have been accumulating exponentially in recent years, due to improvements in molecular biology techniques, X-ray detectors, high-power synchrotrons and nuclear magnetic resonance technology. The PDB was set up at the
Brookhaven National Laboratory in Upton, New York, in order to store such information and make it available to the world scientific community, traditionally via magnetic tape and more recently on compact disks. However, the volume of data had begun to present a problem for those searching the entire collection.

The new browser, developed by Prof. Joel Sussman of the Weizmann Institute and Brookhaven, Dr. Clifford Felder of the Weizmann Institute and Dr. David Stampf of Brookhaven, solves this problem with a utility that enables a complete text search of PDB entries on-line in a user-friendly environment. All components of this browser were written using public domain software, which is freely available to users.

Prof. Sussman, a member of the Institute's Department of Structural Biology, also works at the Brookhaven Laboratory, where he heads the Protein Data Bank. Dr. Felder is a technical assistant in the Institute's Departments of Structural Biology and Chemical Physics.