RCSB PDB Newsletter
Number 21 -- Spring 2004

Published quarterly by the
Research Collaboratory for Structural Bioinformatics
Protein Data Bank

Weekly RCSB PDB news is available online at
www.rcsb.org/pdb/latest_news.html.

Links to RCSB PDB newsletters are available at
www.rcsb.org/pdb/newsletter.html.

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-----------------------------------------
SNAPSHOT -- April 1, 2004

24,908 released atomic coordinate entries

Molecule Type
      22,528 proteins, peptides, and viruses
       1,301 nucleic acids
       1,061 protein/nucleic acid complexes
          18 carbohydrates

Experimental Technique
      21,230 diffraction and other
       3,678 NMR

      12,324 structure factor files
       1,868 NMR restraint files


TABLE OF CONTENTS

Message from the RCSB PDB

Data Deposition and Processing
        PDB Chemical Component Dictionary Format Description Available
        Validation of Protein Structures for the PDB
        PDB Deposition Statistics

Data Query, Reporting, and Access
        Website Statistics
        QuickSearch Available on RCSB PDB Site
        Accessing and Understanding Biological Units

RCSB PDB Outreach
        The PDB: A Case Study in Management of Community Data
        Molecular Machinery Poster Available as PDF
        Art of Science Exhibit Visits the University of Wisconsin-Madison
        Molecules of the Quarter:
            Carbonic Anhydrase, Glycolytic Enzymes, Calcium Pump

PDB Community Focus: Helen M. Berman

RCSB PDB Job Listing

Related Links: File Formats

PDB Education Corner by Tommie S. Hata

Statement of Support
RCSB PDB Leadership Team
RCSB PDB Members


--------------------------------------------
MESSAGE FROM THE RCSB PDB

The National Science Foundation (NSF) has renewed for five years
funding for the PDB under the management of the RCSB. NSF has
supported the PDB continuously since 1975, and a multi-agency support
partnership first formed in 1989. For the past five years, that
partnership has included NSF, the National Institute of General
Medical Sciences (NIGMS), the Department of Energy (DOE), and the
National Library of Medicine (NLM). The partnership has been expanded
now to include the National Cancer Institute (NCI), the National
Center for Research Resources (NCRR), the National Institute of
Biomedical Imaging and Bioengineering (NIBIB), and the National
Institute of Neurological Disorders and Stroke (NINDS).

The new support agreement, which began Jan. 1, calls for the continued
management of the PDB by three members of the Research Collaboratory
for Structural Bioinformatics (RCSB): Rutgers, The State University of
New Jersey; the San Diego Supercomputer Center at the University of
California, San Diego; and the University of Maryland/National
Institute of Standards and Technology's Center for Advanced Research
in Biotechnology. This new era for PDB opens following the recent
announcement of the wwPDB (www.wwpdb.org), an international agreement
to coordinate the deposition and distribution of molecular structure
data.

The PDB has continued to grow and evolve since its inception in
1971. Last year, more than 4,600 new molecular structures were
added. On an average day, visitors download various structural files
more than 120,000 times. During the next five years, the RCSB PDB will
meet challenges that include the expanded integration of its
information with other biological resources, keeping up with the
increasing complexity and volume of deposited structures, meeting the
demands for more complex queries, and providing more detailed
annotation of the experiments and the structures. The PDB will also
continue to serve an ever expanding, diverse and global user
community.


DATA DEPOSITION AND PROCESSING

 	PDB CHEMICAL COMPONENT DICTIONARY FORMAT DESCRIPTION AVAILABLE

The PDB is constantly improving its descriptions of small
molecules. Its Chemical Component Dictionary (formerly called the HET
Group Dictionary) is available in PDB and mmCIF formats, and is
updated weekly. This resource, created by the curation efforts of the
PDB teams at Rutgers University and CARB/NIST, is under active
development. A guide to the formats used in the PDB Chemical Component
Dictionary is available at deposit.pdb.org/cc_dict_tut.html. This
guide provides descriptions and examples of the contents of the PDB
and mmCIF format Chemical Component Dictionaries, as well as a
description of the contents of entries in the Ligand Depot.

Ligand Depot (ligand-depot.rutgers.edu) has been created as a data
warehouse that integrates databases, services, tools, and methods
related to small molecules that are bound to macromolecules. It was
created to help users explore the PDB Chemical Component Dictionary
and the small molecule contents of the PDB. Comments and suggestions
on the PDB Chemical Component Dictionary, the format description
guide, and Ligand Depot are greatly appreciated, and may be sent to
info@rcsb.org.


	VALIDATION OF PROTEIN STRUCTURES FOR THE PDB

A paper published in the Macromolecular Crystallography volume of
Methods in Enzymology describes the procedures used for structure
validation and processing by the PDB. The article is an overview of
the deposition process, including descriptions of the checks and
reports generated by ADIT. The validation and standardization of all
the data in the PDB are also outlined. J. Westbrook, Z. Feng,
K. Burkhardt, H.M. Berman: Validation of protein structures for
protein data bank. Methods Enzymol. (2003) 374: 370-85.

	PDB DEPOSITION STATISTICS

In the first quarter of 2004, approximately 1,273 structures were
deposited in the PDB archive. Of the structures received, 83% were
deposited with a "hold until publication" release status; 3% were
deposited with a specific release date; and 14% were deposited with a
"release immediately" status.

84% of these entries were the result of X-ray crystallographic
experiments; 13% were determined by NMR methods.

	RELEASE OF NEW DEPOSITION TOOL AT BMRB

BioMagResBank (BMRB) and RCSB PDB have jointly released a new ADIT-NMR
deposition tool, which is available from the BMRB website
(www.bmrb.wisc.edu). The current ADIT-NMR release provides the
biological NMR community with a deposition interface for submitting a
wide variety of quantitative experimental results from NMR
spectroscopic studies of biological macromolecules to BMRB. The
interface will be familiar to those who have submitted atomic
coordinates and NMR constraints to the PDB.

ADIT-NMR has been developed as a collaborative project between the
RCSB members PDB and BMRB. Through the PDB/BMRB collaboration, the
ADIT-NMR tool will soon become a one-stop site for the deposition of
all NMR derived data including atomic coordinates and constraints. The
tool combines the BMRB dictionary for NMR experimental results with
the software platform created by the RCSB PDB for the ADIT deposition
system to create an easy to use interface for submitting NMR spectral
parameters (chemical shifts, J-coupling constants, residual dipolar
couplings, etc.), relaxation parameters, hydrogen exchange and pKa
data to the BMRB. All members of the biological NMR community are
encouraged to make use of ADITNMR in depositing their data at the BMRB
and the RCSB PDB.

BMRB is the publicly accessible depository for NMR results from
peptides, proteins, and nucleic acids recognized by the International
Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union
Task Group on the Standardization of Data Bases of Protein and Nucleic
Acid Structures Determined by NMR Spectroscopy.  

DATA QUERY, REPORTING, AND ACCESS

        WEBSITE STATISTICS

The PDB is available from several Web and FTP sites located around the
world. Users are also invited to preview new features at the RCSB PDB
beta test site, accessible at beta.rcsb.org/pdb.

The access statistics are given below for the primary RCSB PDB website
at www.pdb.org.

  Access Statistics for www.pdb.org

	 Daily Average.....Monthly Totals
Month...Hits......Files....Sites.....MBytes....Files.......Hits.....
Jan 04..230,365...173,524..113,681...293,505...5,379,258...7,141,343
Feb 04..266,211...196,747..131,202...222,480...5,508,931...7,453,926
Mar 04..257,754...189,513..120,288...254,218...5,685,405...7,732,636


	QUICKSEARCH AVAILABLE ON RCSB PDB SITE

A new keyword search feature that searches across the PDB archive
and/or the RCSB PDB website static pages is available. It supports the
search syntax of the Lucene-based keyword search currently in
production. An "exact word match" and "full text" search is performed
on an index of the mmCIF files and an index of the static RCSB PDB Web
pages. The structures returned by the search can be browsed, refined,
and explored using the Query Result Browser and Structure
Explorer. The static page results are listed as links and displayed
with the keyword highlighted in the context in which it
appears. Please write to info@rcsb.org with comments or suggestions.

ACCESSING AND UNDERSTANDING BIOLOGICAL UNITS

When crystallographic structures are deposited in the PDB, the primary
coordinate file generally contains one asymmetric unit-a concept that
has applicability only to crystallography, but is important to
understanding the process in obtaining the functional biological
molecule. An introduction to biological units in the PDB archive is
now accessible at www.rcsb.org/pdb/biounit_tutorial.html. This useful
guide:

* Defines "asymmetric unit" and "biological molecule."
* Indicates where information about the biological unit can be found 
  in PDB and mmCIF coordinate files.
* Describes how the biological unit files in the PDB have been derived.

Coordinate files for the biological units for applicable structures
are accessible from the View Structure and Download/Display File
sections of the Structure Explorer pages on the primary PDB website
and its mirrors. The biological unit coordinate files can also be
downloaded from the PDB FTP site at ftp://ftp.rcsb.org/pub/
pdb/data/biounit/coordinates/. Images for the asymmetric and
biological units are available from each entry's View Structure
section of the Structure Explorer page.

RCSB PDB OUTREACH

	MOLECULAR MACHINERY POSTER AVAILABLE AS PDF

The poster, "Molecular Machinery: A Tour of the Protein Data Bank" by
David S. Goodsell, is available as downloadable PDF files, one as a
two-sided, 8 1/2" x 11" quick reference guide (5MB) at
www.rcsb.org/pdb/molecules/poster_quickref.pdf, and the other as a 24"
x 36" poster (31MB) at www.rcsb.org/pdb/molecules/poster_full.pdf.


        ART OF SCIENCE EXHIBIT VISITS THE UNIVERSITY OF
        WISCONSIN-MADISON

The RCSB PDB's Art of Science exhibit, which includes posters from the
Molecule of the Month series, was displayed in the Biochemistry Atrium
at the University of Wisconsin-Madison in February and March. The
exhibit was sponsored by the Center for Eukaryotic Structural Genomics
(CESG) and the BioMagResBank (BMRB).

        THE PDB: A CASE STUDY IN MANAGEMENTOF COMMUNITY DATA

A paper in the inaugural issue of Current Proteomics describes the
development of the PDB and the expansion of its community of data
depositors and users. The lessons learned from the development of the
PDB into a Web-based archive containing approximately 25,000 released
structures and more than 160,000 hits per day may be applicable to the
ongoing development of new data and knowledge resources in proteomics.

H.M. Berman, P.E. Bourne, J. Westbrook: The Protein Data Bank: A case
study in management of community data. Current Proteomics (2004) 1:
49-57.


	PDB MOLECULES OF THE QUARTER:
	CARBONIC ANHYDRASE, GLYCOLYTIC ENZYMES, CALCIUM PUMP

The Molecule of the Month series, by David S. Goodsell, explores the
functions and significance of selected biological macromolecules for a
general audience (www.rcsb.org/pdb/molecules/
molecule_list.html). Three features during this past quarter were:

 * Carbonic Anhydrase: Breathing in, Breathing Out

January, 2004 -- Breathing is a fundamental function in life. In our
lungs, oxygen diffuses into the blood, binds to hemoglobin, and is
transported to all the cells of our body. Carbon dioxide is a
byproduct of sugar and fat breakdown and must be removed from the
body. However, less than 10% of the carbon dioxide that diffuses out
of cells dissolves in the blood plasma, about 20% binds to hemoglobin,
while 70% is converted to carbonic acid to be carried to the lungs.

Carbonic anhydrase, an enzyme in red blood cells, aids in the
conversion of carbon dioxide to carbonic acid and bicarbonate
ions. When red blood cells reach the lungs, the enzyme helps to
convert the bicarbonate ions back to carbon dioxide, which we breathe
out. Since its identification in 1933, carbonic anhydrase has been
found abundant in all mammalian tissues, plants, algae, and
bacteria. This ancient enzyme has three distinct classes -- alpha,
beta, and gamma. While all three require a zinc ion at the active
site, members of one class share very little sequence or structural
similarity with the other two classes, suggesting that each class
evolved independently.

Carbonic anhydrase from mammals belongs to the alpha class, the plant
enzymes belong to the beta class, while the enzyme from
methane-producing bacteria that grow in hot springs forms the gamma
class. PDB entries 1ca2, 1ddz, and 1thj are examples of the alpha,
beta, and gamma carbonic anhydrase enzymes, respectively. The zinc
ions in the active sites are blue. The alpha enzyme is a monomer,
while the gamma enzyme is trimeric. Although the beta enzyme is a
dimer, there are four zinc ions bound to the structure indicating four
possible enzyme active sites.

Since this enzyme produces and uses protons and bicarbonate ions,
carbonic anhydrase plays a key role in the regulation of pH and fluid
balance in different parts of our body. When there is a build up of
the fluid that maintains the shape of our eyes, the fluid often
presses on the optic nerve in the eye and may damage it. This
condition is called glaucoma. In recent years, inhibitors of carbonic
anhydrase have been used to treat glaucoma.

For more information on carbonic anhydrase, see
www.rcsb.org/pdb/molecules/pdb49_1.html

 * Glycolytic Enzymes

February, 2004 -- Glucose is a convenient high-energy fuel for cells
because it is stable, soluble, and easy to transport from storage to
where it's needed. Glycolysis (sugar breaking) is a ten-step cellular
process to burn glucose in small, well-controlled steps to capture the
energy as ATP (adenosine triphosphate).

A glucose molecule is primed with two phosphates (using up two ATP
molecules), broken in two, reshaped, and dehydrated, forming four ATP
molecules in the process, or a net gain of two ATPs. One glycolytic
enzyme removes several hydrogen atoms from the sugar, transferring
them to the small carrier molecule NAD (nicotinamide adenine
dinucleotide). Many cells, including most of our own, eventually
combine the hydrogens with oxygen to form water, building additional
ATP in the process. In a reaction used to make wine and beer, yeast
cells use alcohol dehydrogenase to add the hydrogen atoms back to the
broken sugar molecule, forming alcohol. In extreme exercise, muscles
add the hydrogen atoms back in a different way to form lactic acid.

For more on glycolytic enzymes, see www.rcsb.org/pdb/molecules/pdb50_1.html

 * Calcium Pump

March, 2004 -- Every time we move, our muscle cells use calcium ions
to coordinate a massive molecular effort. These cells release a flood
of calcium ions from a special intracellular container, the
sarcoplasmic reticulum, which surrounds the bundles of actin and
myosin filaments. The calcium ions rapidly spread and bind to
tropomyosins on actin filaments. They shift shape slightly and allow
myosin to bind and begin climbing up the filament, contracting the
muscle.

The calcium pump, found in the membrane of the sarcoplasmic reticulum
(right) from PDB entry 1eul, allows muscles to relax after this
frenzied wave of calcium-induced contraction by pumping calcium ions
back into the sarcoplasmic reticulum. This allows the muscle to
relax. The pump has a big domain poking out of the sarcoplasmic
reticulum, and a region that is embedded in the membrane, forming a
tunnel to the other side. For each ATP broken, the pump transfers two
calcium ions (blue spheres) through the membrane, and two or three
hydrogen ions in the opposite direction.

For more on the calcium pump, see www.rcsb.org/pdb/molecules/pdb51_1.html


PDB COMMUNITY FOCUS: HELEN M. BERMAN 

Helen M. Berman, Director of the RCSB Protein Data Bank, completed an
AB degree in chemistry at Barnard College in 1964, and in 1967
received her PhD in natural science from the University of Pittsburgh
where she studied with George Jeffrey in the Department of
Crystallography. In 1969, she went to the Institute for Cancer
Research (ICR), Fox Chase Cancer Center in Philadelphia to work with
Jenny Glusker. She became an Assistant Member of ICR in 1973 and then
rose through the ranks to Senior Member. She was also an Adjunct
Professor at the University of Pennsylvania and Director of Research
Computing at Fox Chase. In 1989, she moved to Rutgers University where
she currently serves as a Board of Governors Professor of Chemistry
and Chemical Biology.

Dr. Berman's crystallographic studies have focused on nucleic acids,
protein-nucleic acid complexes, and collagen. She has also done
systematic analyses of the hydration patterns of biological molecules,
including nucleic acids and collagen. Since the earliest days of her
career, she has been interested in establishing methods to collect and
archive structural data so that systematic studies of the data could
be facilitated. She was part of the original team that developed the
PDB at Brookhaven National Laboratory in 1971, and in 1991 she founded
the Nucleic Acid Database (NDB; http://ndbserver.rutgers.edu/). In
1998, she led the team of Research Collaboratory for Structural
Bioinformatics (RCSB) members that won the contract to manage the PDB.

Throughout her career, Dr. Berman has been an active participant in
the scientific community. She has served on numerous advisory boards
for the National Science Foundation, the National Institutes of
Health, and on journal editorial boards. She has served as President
of the American Crystallographic Association (ACA) and has also held
leadership positions in the Biophysical Society and the International
Union of Crystallography (IUCr). She received the 2000 Biophysical
Society Award for Distinguished Service and is a Fellow of the
Biophysical Society and of the American Association for the
Advancement of Science.

Under Dr. Berman's leadership, the RCSB began its second five-year
period of PDB management in January 2004. During the first five years,
the number of released structures in the archive had more than
doubled, and the pace of depositions continues to increase at a steady
rate.

The RCSB PDB staff solicited Dr. Berman's views on RCSB PDB's
accomplishments to date, and her vision for the future.

Q: The PDB was born at a Cold Spring Harbor Symposium in 1971. What
was that meeting like?

A: It was an enormously exciting meeting, especially for a young
crystallographer. Virtually all the pioneers of the field were there,
presenting the results of their research. A particularly vivid image I
have is of a large group of people sitting on the grass in a circle
around Max Perutz talking about hemoglobin.


Q: What has shaped the PDB the most the since its beginnings as an
archive containing seven structures?

A: There has been a progression of influences on the PDB. First, the
focus was on getting structures into the PDB. In the 1970s, Tom
Koetzle single handedly wrote personal letters to every protein
crystallographer asking them to participate. In the 1980s, the
community of protein crystallographers began to organize under the
leadership of Fred Richards to try to encourage people to deposit
structures. The IUCr set up more formal committees to achieve the same
thing. In 1989, guidelines were set forth requiring deposition and
release of macromolecular structures. At the same time, the technology
improved making structure determination much faster. By the early
1990s, the number of depositions began to rise quickly and the problem
of how to keep up with the data emerged. A backlog of structures began
to build. The PDB was a victim of its own success. The use of modern
data management methods as well as the development of an efficient
team of annotators has helped to solve this problem. The challenges in
the 2000s will be high throughput structure analysis, large
macromolecular assemblies, and the demand for archiving more
information about each experiment and its results.


Q: You have been actively involved with the PDB since its
beginning. What continues to draw you to this project?

A: The idea that by looking at groups of structures it will be
possible to derive new knowledge has always been a compelling
concept. I have done this in my own research and have always wanted to
make it possible for others. If all the data are organized properly,
it should be possible to mine it efficiently. If many people can do
this on large data sets, it should be possible to learn about basic
concepts, such as protein folding, and use the knowledge to create new
drugs.


Q: Some people think that being involved with scientific
infrastructure, such as the PDB, is not doing real science and is
therefore less important. Do you agree?

A: Not at all. It is one of the most important things that I can
do. To do it right requires knowledge of the data and the technology
needed to collect and disseminate it. Once the infrastructure is in
place, new science will emerge. To facilitate that process and see
what emerges, and to imagine what new science will be facilitated is
what motivates me.


Q: The RCSB is comprised of organizations in different parts of the
country. How does the collaboration work?

A: That is complicated. Each site has its own set of projects that
contribute to the PDB. However, each project must also interact with
all the others. To make this work we have developed various
computer-based forums. Daily communication by email and phone is
critical, as are personal visits and personnel exchanges among the
groups. Recently, we have begun to use video conferencing. Once a year
we have a retreat that allows everyone to be together for a couple of
days to talk about the various projects, to plan for the coming year,
and for PDB staffers to get to know one another.


Q: Who makes up the PDB's user community?

A: It used be only crystallographers, and later NMR spectroscopists,
but now it has expanded to include biologists, computational
biologists, educators, and students.


Q: How does the PDB interact with its users?

A: We have various electronic mail services that allow users to ask
questions and bring problems to our attention. We attend many
different meetings and participate in a variety of ways. At some
meetings, we have an exhibit booth. We are also organizing workshops
for the purpose of educating different parts of the community about
what we do and how to use the various tools. Outreach is a key element
of the PDB because it gives us the feedback we need to improve what we
do.


Q: Recently, the RCSB formalized the ongoing collaboration with the
Macromolecular Structure Database-European Bioinformatics Institute
and PDBj (PDB Japan) to form the wwPDB. How does this affect the PDB?

A: The wwPDB was organized to make sure that the PDB remains as a
single archive. When users from around the world access a flat file
with ID 1XXX they can be assured that they will always get the same
file. This organization will also help us develop new collaborations
that will enhance the use of the PDB files. Science is international
and wwPDB acknowledges that.


Q: Currently, 28 of your structure determinations are in the PDB. What
has been your experience as a PDB depositor?

A: Watching my students deposit files in the PDB allows me to see how
we can improve the process.


Q: You are active in other areas of research, including
protein-nucleic acid interactions, structure determinations, and
databases. Has this activity influenced your work with the PDB?

A: As a depositor and a user, I have both perspectives. I have used
structural data to do systematic analyses of macromolecules. The need
to have easy access to the data was a motivating force for me in
helping to improve the PDB. As a user of the PDB, I can see how we can
make it easier for others to use.


Q: What do you think the PDB will be like in the next 30 years?

A: In 1971, it was almost beyond our imagination that structure
determination of proteins could be completed in a few days with the
results instantly accessible on a desktop computer. But here we are,
and we now know for sure that in the future, there will be even more
structures, new methods for structure determination, much larger
structures and we will have more information about each structure. All
aspects of the process will be fully automated. The really exciting
thing to think about is what people will do with all the data. This
will depend on the ingenuity of new generations of biologists, some of
whom are not yet born, who will certainly find ways to use all this
information and give us the ultimate knowledge about how molecules
function.


RCSB PDB JOB LISTINGS

RCSB PDB career opportunities are posted at
www.rcsb.org/pdb/jobs.html. The current available opening is:

STRUCTURAL BIOINFORMATICS PROJECT LEADER

The Protein Data Bank (PDB) group at the University of California, San
Diego is seeking a Project Manager to guide the PDB in its next
five-year phase of development. The Project Manager will work
collaboratively with the PDB software architects, programmers, and
scientists, at UCSD and the RCSB PDB partner sites, to expand the
PDB's functionality and reliability as a premier biological data and
information resource.

Job functions include: identify and develop requirements for new PDB
delivery, query functionality and usability; develop and implement
innovative approaches that will satisfy users' current needs and
anticipate their future needs based on progress in the science of
structural biology and structural bioinformatics; and work with the
scientific community to fulfill the above.

Qualifications: 

* Ph.D. in biological sciences or related field or equivalent
  combination of education and experience in the field of
  bioinformatics and computational biology, including expert knowledge
  and research experience in sequence and protein structure analysis,
  protein 3-D structure prediction and fold recognition, and protein
  modeling.
* Extensive background and expertise in project management and
  research coordination.
* Demonstrated experience working with a team of high-level
  professional scientists and computer programmers.
* Advanced skills and experience in developing biological databases
  and in SQL.
* Ability to communicate and deal effectively and productively with
  people at all levels of responsibility in various functional areas.
* Demonstrated ability to work with a diverse set of people to solve
  problems and build consensus.
* Strong, demonstrated experience in software development, especially
  with Enterprise Java and multi-tier architectures.

Applicants should apply on-line at
joblink.ucsd.edu/bulletin/job.html?cat=new&job_id=31324.

BIOCHEMICAL INFORMATION SPECIALIST

The Protein Data Bank at Rutgers University has a position open for a
Biochemical Information Specialist to curate and standardize
macromolecular structures for the Protein Data Bank. A background in
biological chemistry, as well as some experience with UNIX-based
computer systems, is required. Experience in crystallography and/or
NMR spectroscopy is a strong advantage. The successful candidate
should be well-motivated, able to pay close attention to detail, and
meet deadlines. This position offers the opportunity to participate in
an exciting project with significant impact on the scientific
community.  Please send resume to Dr. Helen Berman at
pdbjobs@rcsb.rutgers.edu.

RELATED LINKS: FILE FORMATS

www.rcsb.org/pdb/info.html#File_Formats_and_Standards

The RCSB PDB offers links to software tools and descriptive resources
for file formats used to describe PDB data. A few of these links
include:

mmCIF Resources deposit.pdb.org/mmcif/ 
Background information, Data Dictionaries (including the PDB Exchange
Dictionary), Proposed Data Items for Structural Genomics Depositions,
mmCIF-PDB correspondences, OMG CORBA API, and software tools

Chemical Component Dictionary and Description
The PDB Chemical Component Dictionary (formerly the HET Group
Dictionary) is available in PDB and mmCIF formats. A guide to these
dictionaries is available at deposit.pdb.org/cc_dict_tut.html

PDB File Format Contents Guide Version 2.2
www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
A description of the PDB file format.


PDB EDUCATION CORNER BY TOMMIE S. HATA

PDB's Education Corner features a different teacher each quarter,
offering an account of how he or she uses the PDB to educate
students. This quarter's column is by Tommie Hata, a biology teacher
at The Pingry School in Martinsville, NJ.

The Protein Data Bank has become a significant and popular website to
supplement our curriculum within molecular biology. Despite attempts
by textbooks to invigorate material with animations and CD-ROM
presentations, the material in a book is often static and disconnected
from the real world of science. The PDB has given life to molecules,
the people behind them, and the process of discovering them.

The Pingry School is a special place. It is a country day school that
offers many opportunities to the student body. The students are
involved in a number of diverse activities from glass blowing to
biomolecular modeling in addition to the standard academic rigor. Our
students have a variety of backgrounds and interests, yet have a
unifying theme in a motivated attitude towards learning and
achieving. The ninth grade biology program at our school has made a
distinct effort to reduce the breadth of the curriculum and improve
the depth of knowledge. This concept has led away from copious note
taking on many broad topics within biology and deeper exploration of
the process of science. The PDB has truly made this possible.

The first unit within our curriculum is the structure and function of
macromolecules. When students are learning the specifics of protein
structure, they predict a structure of a retinol binding protein (RBP)
and use the PDB (1aqb) to compare their predicted structure to an
actual RBP. The students look specifically for the hydrophobic nature
in amino acids within the "carrying" portion of the molecule, as
compared to hydrophilic portion of the molecule, using computer
programs such as MDL Chime and RasMol.

The reality of seeing the amino acids in a three dimensional form,
comparing different records of RBP, and manipulating the molecule
using chime led to many to exclaim "Ahaa!" or "I was right!" and
facilitate discussions on the other possibilities of structure.

Using Boolean commands in RasMol, such as "sidechain and alpha" or
"backbone and helix," further increases the students' awareness of
protein structure. On separate occasions, students have generated
RasMol scripts to highlight individual amino acid sidechains in
hemoglobin that interact with the heme group and to highlight cAMP
bound within catabolite activator protein (CAP). The educator is
simply a tool in the learning process; the students are given the
resources to facilitate learning.

The Molecule of the Month feature by Dr. David Goodsell has been
integral to deepening knowledge of other biological molecules and
processes. Almost every unit is supplemented by having the students
read a feature and then answer questions developed by the
teachers. Topics such as cellular respiration, photosynthesis, gene
regulation, and membrane transport relate to Molecule of the Month
features. Some students take the next step to view and analyze the PDB
files referenced in the features and compared different records.

In September, The Pingry School established a Students Modeling A
Research Topic (SMART) team under the guidance of
Dr. Tim Herman at the Milwaukee School of Engineering (see PDB
Education Corner from Summer 2003 issue). With help from Dr. Richard
Ebright (HHMI/Waksman Institute/Rutgers), Dr. Helen Berman, and other
scientists at the PDB, my seven students have been able to design a
physical model of a class I transcription-activation complex
(www.mybiology.com/smartteam.htm).

College-level concepts such as protein structural motifs have become
part of our discussions, which would not have been possible without
the PDB. Through their interaction with Dr. Berman and the PDB, the
students also gain a better understanding and appreciation for both
the science and scientists involved in crystallography.

In addition to becoming a tool used in our classroom, the PDB has made
scientists and their work tangible to our students. At Pingry, the PDB
has morphed from a tool exclusive to the science community to a
shortcut on the students' computer desktops. 

-----------------------------------------
STATEMENT OF SUPPORT

The RCSB PDB is supported by funds from the National Science
Foundation, the National Institute of General Medical Sciences, the
Department of Energy, the National Library of Medicine, the National
Cancer Institute, the National Center for Research Resources, the
National Institute of Biomedical Imaging and Bioengineering, and the
National Institute of Neurological Disorders and Stroke.

-----------------------------------------
The RCSB PDB is managed by three partner sites of the Research
Collaboratory for Structural Bioinformatics:

RUTGERS
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The overall operation of the PDB is managed by the 
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support is provided by the RCSB PDB Members.


RCSB PDB LEADERSHIP TEAM

Dr. Helen M. Berman - Director
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berman@rcsb.rutgers.edu

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bourne@sdsc.edu

Judith L. Flippen-Anderson - Production and Outreach Leader
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Dr. Gary L. Gilliland - Co-Director
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Dr. John Westbrook - Co-Director
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RCSB PDB MEMBERS

RUTGERS

Prentice Bisbal
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Li Chen
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SDSC/UCSD

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CARB/NIST

Al Carlson
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Dr. Veerasamy Ravichandran
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Kathryn Rosecrans
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Elizabeth Walker
walkere@umbi.umd.edu

-----------------------------------------
RCSB PDB Newsletter
Number 21 -- Spring 2004

Published quarterly by the
Research Collaboratory for Structural Bioinformatics
Protein Data Bank

Weekly RCSB PDB news is available online at
www.rcsb.org/pdb/latest_news.html.

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