RCSB PDB Newsletter Archive
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Editions for 2013
Issue 59 - October 2013
This newsletter describes the recent wwPDB Symposium: A Celebration of Open Access in Structural Biology, recent deposition and website statistics, ligand report options, new features added to the RCSB PDB and PDB-101 websites, and an update on the new wwPDB Deposition & Annotation System.
Issue 58 - July 2013
Highlights wwPDB News, upcoming meetings, and more.
The Education Corner highlights the RCSB PDB's visit to the National Science Teachers Association meeting.
Issue 57 - April 2013
Describes new website features, the Biologically Interesting molecule
Reference Dictionary, and more. The Education Corner highlights the RCSB PDB help desk.
Issue 56 - January 2013
Explores the 2012 Annual Report, 2012 deposition and access statistics,
how to visually map PDB structures to sequences, and more. The Education
Corner describes molecular visualization tools developed for browers and
mobile devices by Takanori Nakane (Kyoto University). Nakane's program NDKmol is part of the
RCSB PDB Mobile app.
Editions for 2012
Issue 55 - Fall 2012
heads back to school with PDB-101, looks at deposition tools pdb_extract and SF-Tool, and
describes the RCSB PDB Mobile app. The Education Corner details the University of Georgia's
Biotech Boot Camp for high school teachers.
Issue 54 - Summer 2012
explores new website features, RCSB PDB Mobile, and 150 Molecule of the Month columns.
The Education Corner looks at how students are Learning Science by Doing Science at the
Waksman Student Scholars Program.
Issue 53 - Spring 2012
includes a look at a special molecular animation, depositing structures for Foldit,
browsing the PDB archive, and more. The Education Corner discusses Project CRYSTAL:
Crystallographers Researching with Young Scientists, Teaching and Learning.
Issue 52 - Winter 2012
Highlights 2011 statistics for deposition and distribution, the latest wwPDB News, and
quick searching at the RCSB PDB website. In the Education Corner, the 2011 RCSB PDB Poster Prize
awardees describe how they are Learning to Become a Structural Biologist. The newsletter also
describes the many ways users can search for ligands and for homo- and hetero-multimer structures,
Molecule of the Month developments, and more.
Editions for 2011
Issue 51 - Fall 2011
Explores the new pdb_extract and SF-Tool updates, the latest website release, new additions to PDB-101,
and the latest on the PDB40 symposium. In the issue's Education Corner, Christopher Smith (Center
for Theoretical Biological Physics at UCSD) gives his Insights into Molecular Modeling for the Middle
Schooler. The newsletter also describes the many ways users can explore new entires, recent RCSB PDB
poster prize awardees, new website and deposition statistics, and more.
Issue 50 - Summer 2011
This issue highlights PDB 40's program, poster session, and travel awards along with the latest developments in data deposition, data query, and
outreach and education. The Education Corner focuses on the American Association for the Advancement of Science's
report Vision and Change in Undergraduate Biology Education: A Call to Action.
The newsletter also describes new options for generating Validation Reports, and highlights the
Browse Database option of exploring the PDB archive using hierarchal trees organized by GO terms,
EC number, source organism, and more.
Issue 49 - Spring 2011
This issue highlights the upcoming PDB 40 symposium, synchrotron news, options available for exploring PDB entries, and more. In the
Education Corner, New Jersey high school teacher Richard Tempsick describes how he builds proteins structures and uses the Molecule of
the Month in the classroom.
Issue 48 - Winter 2011
The year 2010 through data deposition, website traffic, and Molecules of the Month. This issue also highlights
the latest website release, recent meeting activities, the 2010 Annual Report PDF, and more.
Editions for 2010
Issue 47 - Fall 2010
This issue highlights the Molecule of the Month and the topic categories.
In the Education Corner, Joan Kiely (Stony Brook University ) describes the Stony Brook University Protein Challenge,
a competition for high school students that helps them understand the structure and function of proteins.
Issue 46 - Summer 2010
This issue highlights new website advanced search and reporting options.
In the Education Corner, Phil McFadden (Oregon State University) describes Protein Portraits, a
nontraditional college course developed around the question of what it might be like to shrink to the
nanometer realm for a direct encounter with a protein molecule.
Issue 45 - Spring 2010
This issue highlights new website features and the comprehensive suite of RCSB PDB training materials.
In the Education Corner, A Proficiency Rubric for Biomacromolecular 3D Literacy is presented.
Issue 44 - Winter 2010
This issue highlights 2009 deposition, release, and access statistics, describes new website
features for searching and reporting, and reviews recent outreach activities. In the
Education Corner, IJsbrand M. Kramer discusses the benefits of using more "realistic"
molecular images in university cell biology courses.
Editions for 2009
Issue 43 - Fall 2009
In the Education Corner, Gary Battle reports on a recent symposium that demonstrated the different ways t
he Cambridge Structural Database is used to teach chemistry. In the Community Focus, Roland Dunbrack,
Jr. (Fox Chase Cancer Center) discusses his research in computational structural biology and the
software his laboratory makes available for download.
Issue 42 - Summer 2009
The new features and functionality that have been added to
www.pdb.org are highlighted.
In the Community Focus, Gregory Warren discusses the worlds of modeling and crystallography.
Recent outreach activities, along with data deposition and data query news, are also available.
Issue 41 - Spring 2009
In this issue, David Goodsell interviews molecular animators Gaël McGill and Graham Johnson to find
out how PDB data gets translated into their detailed movies and images. In the Education Corner,
Gavin Whittaker describes how physical models can be created and used to provide a unique view of
molecular structure. New RCSB PDB features and developments, including the recent release of
MyPDB email alerts, are highlighted.
Issue 40 - Winter 2009
This edition offers tips for depositing multiple related
structures and describes the release of PDB Archive Version 3.15.
Deposition and website statistics for 2008, the domain annotations in
3D view, the release of the 2008 Annual Report, and the publication of
a new resource for learning about PDB Data, called Looking at Structures, are described.
In this quarter's Education Corner, Bernadette Uzzi talks about
protein structure-related courses available from Brookhaven National
Laboratory's Science Learning Center. In the Community Focus, Johannes
Kirchmair and Gerhard Wolber (University of Innsbruck) discuss their
paper The Protein Data Bank (PDB), Its Related Services and Software Tools
as Key Components for In Silico Guided Drug Discovery, and more.
Editions for 2008
Issue 39 - Fall 2008
This edition describes how Ligand Expo can be used to deposit structures, and
announces the Comprehensive Format Guide for the PDB File Format (Version 3.2).
Other highlights include the enhanced RSS feed for PDB structures and searches
based on PubMed abstracts at the RCSB PDB website. In this quarter's Education
Corner, Brad Larson (Sunset Lake Software) talks about the origin and applications
of the iPhone program Molecules. In the Community Focus, Paul D. Adams
(Lawrence Berkeley Laboratory) discusses PHENIX, the Technology Port of the PSI
Structural Genomics Knowledgebase, and his work at the Joint BioEnergy Institute.
Issue 38 - Summer 2008
This edition highlights new deposition tools, such as SF-Tool and
Ligand Expo, and explores usage statistics for PDB data. The New
Jersey and National Protein Modeling events at the Science Olympiad
are described, along with recent presentations and publications. In
this quarter's Education Corner, Judy Voet (Swarthmore) and Donald
Voet (University of Pennsylvania) discuss Biochemistry and Molecular
Biology Education (BAMBED), a Journal for University, College, and
High School Educators. John Norvell (NIGMS) discusses his career,
NIGMS, and the ProteinStructure Initiative.
Issue 37 - Spring 2008
PDF formats, this issue
highlights deposition tools, different types of statistics about data
in the PDB archive, and recent outreach activities. In the Education
Corner, Jeramia Ory (Kings College) describes how he uses Chimera to
create molecular multimedia in his classroom. Christine Orengo
(University College London) is the subject of this quarter's Community
Focus, where CATH and other research projects are described.
Issue 36 - Winter 2008
Published in a sleek new
HTML format and also in
PDF, this issue describes a new
version of ADIT that was developed to improve data accuracy and
consistency, new outreach programs, and the publication of the 2007
Annual Report. The Community Focus looks at this year's New Jersey
Science Olympiad competition, and in the Education Corner, Teresa
MacDonald (The University of Kansas Natural History Museum) describes
edible protein models.
Editions for 2007
Issue 35 - Fall 2007
PDF formats, this issue's
"Message from the RCSB PDB" looks back at the many recent RCSB PDB-
and wwPDB-related meetings. The newsletter also describes the "5 Easy
Steps for Data Deposition with ADIT" that were presented at this past
summer's ACA meeting. New features and enhancements added to the RCSB
PDB website and database are reviewed. This quarter's Education Corner
by Melissa Kosinski-Collins (Brandeis University) explores the Java
program StarBiochem and how it can be used independently by students
to view the structure and function of proteins and nucleic acids. The
Community Focus interview speaks with RCSB PDB Co-Director Phil Bourne
about his involvement with the computational, systems biology, and
Issue 34 - Summer 2007
PDF formats, this issue looks
at the release of the remediated PDB archive, tools for depositing
structures, and new features of the RCSB PDB website. This quarter's
Education Corner by Alisa Zapp Machalek describes educational
resources available from the NIGMS. In the Community Focus interview,
Alex Wlodawer of the National Cancer Institute discusses his recent
thoughts on the deposition of experimental data files, and his
thoughts on reviewing macromolecular structure papers for publication
Issue 33 - Spring 2007
PDF formats, Article highlights
include upcoming meeting participation, deposition statistics
(including experimental data) for the first quarter of 2007, and new
additions to the BioSync resource. The issue also presents new
features of the RCSB PDB website, including improved access to ligand
data, a tool for viewing protein-ligand interactions, new advanced
search options, and more. This quarter's Education Corner looks at the
New Jersey Science Olympiad competition. The Community Focus
interviews Angela Gronenborn, an NMR spectroscopist who is the
Rosalind Franklin Professor and Chair of the Department of Structural
Biology at the University of Pittsburgh.
Issue 32 - Winter 2007
PDF formats, this newsletter
describes new developments in data deposition and processing,
including an article on how DOIs are available for released entries in
the PDB archive. The issue also looks at how search results and
tabular reports can be sorted, different methods for exploring protein
structure domains, and how to search for sequence variants. In this
quarter's Education Corner, Gary L. Gilliland reports on the X-Ray
Methods in Structural Biology Course held at Cold Spring Harbor
Laboratory. In the Community Focus interview, the RCSB PDB speaks with
Julian Voss-Andreae, a sculptor of protein structures.
Editions for 2006
Issue 31 - Fall 2006
PDF formats, this newsletter
describes new developments in data deposition tools, how to use
Protein Workshop to view PDB structures, and the recently added RCSB
PDB Poster Prizes. In this quarter's Education Corner, Robert J.
Warburton describes ways of seeing and thinking about PDB structures,
and Wah Chiu discusses the future of cryo-electron microscopy in the
Issue 30 - Summer 2006
PDF formats, this issue of the
newsletter describes new developments, including pdb_extract for NMR
depositions, Web Services, scripts for downloading PDB data, and the
RSS feed for new structures. In this quarter's Education Corner,
Cheryl Campbell describes her path to the PDB, and Michael G. Rossmann
discusses his scientific career in the Community Focus.
Issue 29 - Spring 2006
PDF formats, article highlights
include a description of how validating structures saves overall
deposition time, and a look at the online table of structures solved
by multiple techniques. This quarter's Education Corner describes how
the RCSB PDB was able to guide middle school students in making
handheld models of the common cold. Also in this issue, Shri C. Jain
describes his scientific career, from determining structures to
training annotators at the RCSB PDB.
Issue 28 - Winter 2006
The Winter 2006 issue of the RCSB PDB Newsletter has been published in
HTML and PDF formats. Highlights include a look at the Tools and
resources at the new RCSB PDB site; Workshop for High School Teachers
and Students: Building Protein Models at the Science Olympiad; a
Community Focus discussion with Frank Allen, Cambridge
Crystallographic Data Centre, and an Education Corner interview with
Margaret A. Franzen (Pellissippi State Technical Community College,
Knoxville, TN) where she discusses how her innovative classroom
teaching methods focus on developing analytical thinking skills and
exposing her students to the process of science. Also available in
Editions for 2005
Issue 27 - Fall 2005
The Fall 2005 issue of the RCSB PDB Newsletter has been published in
HTML and PDF formats. Highlights highlights include a look at the new
site that became the main RCSB PDB site on January 1, 2006; a
Community Focus discussion with William L. Duax (International Union
of Crystallography and Hauptman-Woodward Medical Research Institute),
and an Education Corner interview with Miriam Rossi (Vassar College)
where she discusses an interdisiplinary course that familiarizes
students with basic concepts of molecular structure, from an
introduction to X-ray crystallographic methods through interpreting
published structural papers. Also available in
Issue 26 - Summer 2005
Robert M. Sweet (Brookhaven National Laboratory) speaks to the RCSB
PDB in this quarter's
Community Focus; Gary Graper (Wisconsin Science Olympiad)
describes the Protein Modeling Event for high school students; and
files from the data uniformity project are released in PDBML/XML
format. Also available in
Issue 25 - Spring 2005
Highlights from this issue include a "Community Focus" look
at Stephen K. Burley (Structural GenomiX, Inc.) and an "Education
Corner" story illustrating a short history of PDB structure
visualization. This issue highlights additional beta site features and
the pdb archive. Also available in
Issue 24 - Winter 2005
Highlights from this issue include a "Community Focus" look at John L.
Markley (BMRB and Center for Eukaryotic Structural Genomics) and an
"Education Corner" story about early protein structures painted on a
wall at RCSB-Rutgers. This issue highlights some beta site features,
and summarizes statistics about structures deposited to the PDB in
2004. Also available in
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Editions for 2004
Issue 23 - Fall 2004
This quarter's "Community Focus" speaks with Haruki Nakamura of PDBj,
and the Education Corner reviews the "X-ray, Molecules, and You"
educational workshop held as part of the ACA meeting. Links related to
the "Database Challenges in Biology" are highlighted. Also available
Issue 22 - Summer 2004
Highlights from this issue include a "Community Focus" article
featuring E-MSD group leader Kim Henrick, and an "Education Corner"
installment by J. Ricky Cox (Murray State University) that discusses
using Visualization Tools in the classroom. The new beta site is
described. Also available in
21 - Spring 2004
This quarter's "Community Focus" speaks with Helen M. Berman of the
RCSB PDB, and the Education Corner is by Tommie S. Hata of The Pingry
School. Links related to the File Formats are highlighted. Also
20 - Winter 2004
This quarter's "Community Focus" speaks with Edward N. Baker,
University of Auckland, and the Education Corner is by Katherine
Kantardjieff from California State University Fullerton. FTP resources
are highlighted. Also available in
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Editions for 2003
19 - Fall 2003
This quarter's "Community Focus" speaks with Brian W. Matthews,
University of Oregon, and the Education Corner is by Paul A. Craig,
Rochester Institute of Technology. Also available in
18 - Summer 2003
This quarter's "Community Focus" speaks with Frances C. Bernstein, and
the Education Corner is by Tim Herman, Center for BioMolecular
Modeling. Software resources are highlighted. Also available in
17 - Spring 2003
The Education Corner is by Gale Rhodes, University of Southern Maine.
Education resources are highlighted. Also available in
16 - Winter 2003
Also available in
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Editions for 2002
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Editions for 2001
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Editions for 2000
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Editions for 1999
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BNL PDB newsletters September 1974 - February
This directory in the FTP archive contains the PDB newsletters
produced at BNL between April 1993 and February 1999.
It also contains PDF files of PDB
newsletters produced at BNL between September 1974 and January 1993.
Please note that the quality of these documents, scanned in their
current condition, reflects the technology available at their time of
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