Issue 44 - Winter 2010
(HTML |
PDF)
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
(HTML |
PDF)
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
(HTML |
PDF)
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
(HTML |
PDF)
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
(HTML |
PDF)
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
(HTML |
PDF)
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
(HTML |
PDF)
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
Published in
HTML and
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
Published in
HTML and
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
educational communities.
Issue 34 - Summer 2007
Published in
HTML and
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
in journals.
Issue 33 - Spring 2007
Published in
HTML and
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
Published in
HTML and
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
Published in
HTML and
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
Community Focus.
Issue 30 - Summer 2006
Published in
HTML and
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
Published in
HTML and
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
PDF
format.
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
PDF
format.
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
PDF
format.
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
PDF
format.
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
PDF
format.
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
in
PDF
format.
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
PDF
format.
Issue
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
available in
PDF
format.
Issue
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
PDF
format.
Issue
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
PDF
format.
Issue
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
PDF
format
Issue
17 - Spring 2003
The Education Corner is by Gale Rhodes, University of Southern Maine.
Education resources are highlighted. Also available in
PDF format.
Issue 13 - Spring 2002
Contains an article about Richard E. Dickerson's equation to describe
the exponential growth for solved crystal structures. Also available
in
PDF format.
BNL PDB newsletters – September 1974 - February
1999
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
production.
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