wo papers have been published online that describe the TargetDB and Ligand Depot resources. TargetDB is a centralized target registration database that includes protein target data from the NIH structural genomics centers and a number of international sites (http://targetdb.pdb.org/). Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids (http://ligand-depot.rutgers.edu/).

TargetDB: a target registration database for structural genomics projects Li Chen, Rose Oughtred, Helen M. Berman, and John Westbrook Bioinformatics: http://bioinformatics.oupjournals.org/cgi/content/abstract/bth300v1

Ligand Depot: a data warehouse for ligands bound to macromolecules Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, and John Westbrook Bioinformatics: http://bioinformatics.oupjournals.org/cgi/content/abstract/bth214v1

The history of the PDB is used to highlight practices important to developers of current biological databases in an article published in the journal Briefings in Bioinformatics. The role of the "human factor" in the form of users, collaborators, scientific societies, and ad hoc committees is also included.

Philip E. Bourne, John Westbrook, Helen M. Berman The Protein Data Bank and lessons in data management (2004) Briefings in Bioinformatics (http://www.henrystewart.com/journals/bib/) 5, pp 23-30.


hanks to the students and judges who participated in the competition for the best student poster presentation in the category of "Protein Structure" at the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004; March 27-31, San Diego, CA).

The RCSB PDB Poster Prize was awarded to Boris E. Shakhnovich for the poster "Protein Structure and Evolutionary History Determine Sequence Space Topology"(Boris E. Shakhnovich(1), Eric Deeds(2), Charles Delisi(1) and Eugene I. Shakhnovich(3))(1)Bioinformatics Program, Boston University; (2)Department of Molecular and Cellular Biology, Harvard University; (3)Department of Chemistry and Chemical Biology, Harvard University

Information about the 2004 RCSB PDB Poster Prize is at http://www.rcsb.org/pdb/poster_prize.html.


he RCSB PDB exhibited with a tabletop display at the 45th Experimental Nuclear Magnetic Resonance Conference (ENC) that was held April 18 - 23 at the Asilomar Conference Center (Pacific Grove, CA).

At RECOMB, the RCSB PDB demonstrated the reengineered website in addition to awarding the RCSB PDB Poster Prize award.

The RCSB PDB participated at the National Science Teachers Association (NSTA) National Convention April 1-4, 2004 in Atlanta, GA. Molecule of the Month materials were made available at the MSOE Center for BioMolecular Modeling's exhibit booth. SMART teams (see Education Corner from Spring 2004) presented their models built from PDB coordinates at the meeting.


short online questionnaire was emailed to 1450 RCSB PDB CD-ROM subscribers in February 2004. The purpose of this instrument was to get to know subscribers, ask their opinion on how well we are doing and gauge interest in a DVD data product.

The questionnaire had a 23% response rate with an approval rating of 84.5%. Many respondents provided additional information in the comments section and took additional time to write us separately.

Problems are being addressed immediately. Suggestions for improvements are being reviewed and considered by RCSB PDB staff. Suggested improvements already in development include a top level index and a DVD data product. The results of the questionnaire have been compiled and are detailed in the CD-ROM Subscriber Questionnaire Results report (http://www.rcsb.org/pdb/2004CDUserReport.html).


wo products were distributed for the April 2004 CD-ROM. Release 108U contained the incremental set of experimentally determined structures (1,490) and models (84) deposited between January 1, 2004 and April 1, 2004, on a single CD-ROM disk. Release 108U-EXP contains the experimental data, both X-ray structure factors (865) and NMR constraints (83), deposited between January 1, 2004 and April 1, 2004, on a single CD-ROM disk. Questions should be directed to pdbcd@rcsb.org. Ordering information is available at http://www.rcsb.org/pdb/cdrom.html.


he Molecule of the Month series, by David S. Goodsell, explores the functions and significance of selected biological macromolecules (www.rcsb.org/pdb/molecules/molecule_list.html). Structures highlighted during this past quarter were:

Growth Hormone: April 2004 -- As children grow, their height, weight and strength increase. Numerous factors influence this growth, including the genetic makeup of the child, nutrition and environmental factors. Specific messengers released by the body also stimulate and regulate growth. Growth hormone is one key growth signal released from the pituitary, a pea-sized gland located at the base of the brain. Lack of this hormone in children can cause them to remain shorter than average, while in its excess they may grow taller than most. Growth hormone continues its work in adults, playing an important role in repair and maintenance of different tissues in the body.

The pituitary releases several hormones including growth hormone, prolactin and placental lactogen. These small protein hormones are similar in their sequence and structure and play crucial roles in growth, development and milk production.

Growth hormone travels through the blood and stimulates the liver to produce a protein called insulin-like growth factor (IGF-1), as in PDB entry 1h02. IGF-1 helps the cartilage cells located at the ends of long bones to multiply. In children, this leads to growth in the length of the bones and increases the child's height. By puberty, however, the cartilage at the ends of most long bones is converted to bone and subsequent action of growth hormone or IGF-1 usually cannot increase their length. IGF-1 also acts on immature muscle cells to increase muscle mass. Aside from these growth stimulating functions, growth hormone participates in regulating the body's metabolism. It acts on fat cells to reduce the amount of stored fats, promotes protein synthesis in cells and plays a role in regulating the sugar levels in the blood. Thus growth hormone has multiple effects on the overall form and function of a growing body.

For more information on growth hormone, by Shuchismita Dutta and David S. Goodsell, see www.rcsb.org/pdb/molecules/pdb52_1.html.

Serpins: May 2004 -- Our cells are often forced to work with dangerous machinery. For instance, cells build many machines for demolition, such as nucleases that break down DNA and RNA, amylases and related enzymes that break down carbohydrates, lipases that chew up lipids, and proteases that disassemble proteins. These destructive enzymes are needed in many capacities. They are used in digestion to break food molecules into workable pieces. They are used in defense to attack invading viruses and bacteria. They are used to break down defective or obsolete molecules inside cells. They are also used in signaling cascades to activate signaling molecules instantly when a message is received. These enzymes are essential when used at the proper place and time, but can spell disaster if they get loose.

To control these destructive machines, our cells also build a host of proteins that block their action and neutralize the danger. The serpins are one class of these molecules, designed to seek out and destroy specific serine proteases. The name serpin, although sounding like something from Greek mythology, is taken from their function: SERine Protease INhibitors. An example is alpha1-antitrypsin, from PDB entry 1psi. It is found in the bloodstream, where it protects the surrounding tissues from the protein-cutting enzyme elastase. Neutrophils (a type of white blood cell) secrete elastase in sites of inflammation, where it breaks down connective tissue and allows blood cells to enter and do their jobs in defense and repair. The serpin protects the neighboring areas and ensures that the elastase doesn't spread throughout the body.

Over thirty different human serpins (a number of which are available in the PDB) have been studied, each with a different essential job. Many are found in the blood. Several control the process of blood clotting: antithrombin limits the action of thrombin when a clot is forming, and antiplasmin limits the action of plasmin when blood clots are being disassembled. Other serpins control the action of proteases used in the complement system, which protects us from bacterial infection.

For more information on serpins, see www.rcsb.org/pdb/molecules/pdb53_1.html.

Acetylcholinesterase: June, 2004 -- Every time you move a muscle and every time you think a thought, your nerve cells are hard at work. They are processing information: receiving signals, deciding what to do with them, and dispatching new messages off to their neighbors. Some nerve cells communicate directly with muscle cells, sending them the signal to contract. Other nerve cells are involved solely in the bureaucracy of information, spending their lives communicating only with other nerve cells. But unlike our human bureaucracies, this processing of information must be fast in order to keep up with the ever-changing demands of life.

Nerves communicate with one another and with muscle cells by using neurotransmitters. These are small molecules that are released from the nerve cell and rapidly diffuse to neighboring cells, stimulating a response once they arrive. Many different neurotransmitters are used for different jobs: glutamate excites nerves into action; GABA inhibits the passing of information; dopamine and serotonin are involved in the subtle messages of thought and cognition. The main job of the neurotransmitter acetylcholine is to carry the signal from nerve cells to muscle cells. When a motor nerve cell gets the proper signal from the nervous system, it releases acetylcholine into its synapses with muscle cells. There, acetylcholine opens receptors on the muscle cells, triggering the process of contraction. Of course, once the message is passed, the neurotransmitter must be destroyed, otherwise later signals would get mixed up in a jumble of obsolete neurotransmitter molecules. The cleanup of old acetylcholine is the job of acetylcholinesterase.

For more information on acetylcholinesterase, see www.rcsb.org/pdb/molecules/pdb54_1.html.