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

Summer 2008
Number 38

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Data Deposition
SF-Tool: A Tool for Crystallographic Experimental Data Validation
Ligand Expo: A Small Molecule Resource
Workshop on Next Generation Validation Tools for the wwPDB
Deposition Statistics
Data Query, Reporting and Access
Website Statistics
Secondary Structure Information
RCSB PDB Usage Statistics
Outreach and Education
RCSB PDB Meetings and Presentations
RCSB PDB Poster Prize Awarded at ACA Meeting
Princeton High School Students Win New Jersey Science Olympiad Protein Modeling State Finals
Congratulations to National Tournament Champions
Papers Published
Structural Displays
Education Corner
Biochemistry and Molecular Biology Education, a Journal for University, College, and High School Educators by Judith G. Voet and Donald H. Voet
PDB Community Focus
John Norvell, Ph.D., National Institute of General Medical Sciences


Biochemistry and Molecular Biology Education (BAMBED)
, a Journal for University, College, and High School Educators by Judith G. Voet1 and Donald H. Voet2, BAMBED Co-Editors-in-Chief

Donald Voet received a B.S. in Chemistry from the California Institute of Technology, a Ph.D. in Chemistry from Harvard University with William Lipscomb, and did postdoctoral research in the Biology Department at MIT with Alexander Rich. As an associate professor at the University of Pennsylvania, Dr. Voet uses X-ray crystallography to study the structure of biologically interesting molecules, including yeast inorganic pyrophosphatase and granulocyte-macrophage colony-timulating factor.

Judith ("Judy") Voet received her B.S. in Chemistry from Antioch College and her Ph.D. in Biochemistry from Brandeis University with Robert H. Abeles. She has done postdoctoral research at the University of Pennsylvania, Haverford College, and the Fox Chase Cancer Center. Dr Voet is the James H. Hammons Professor, Emeritus, at Swarthmore College. Her main area of research involves enzyme reaction mechanisms and inhibition.

This husband and wife team serve as joint editors-in-chief of the journal Biochemistry and Molecular Biology Education (BAMBED), published by John Wiley & Sons for the International Union of Biochemistry and Molecular Biology (IUBMB). They have also co-authored the seminal textbook Biochemistry, now in its third edition, and Fundamentals of Biochemistry, along with Charlotte Pratt, now in its third edition.

  1. Chemistry Department, Swarthmore College,
    Swarthmore, PA 19081
  2. Chemistry Department, University of Pennsylvania,
    Philadelphia, PA 19104

The aim of Biochemistry and Molecular Biology Education (BAMBED) is to enhance teacher preparation and student learning in biochemistry, molecular biology, and related sciences such as biophysics and cell biology, by promoting the worldwide dissemination of educational materials. BAMBED seeks and communicates articles on many topics, including:

  • innovative techniques in teaching and learning,
  • new pedagogical approaches,
  • research in biochemistry and molecular biology education,
  • reviews on emerging areas of biochemistry and molecular biology to provide background for the preparation of lectures, seminars, student presentations, dissertations, etc.,
  • historical reviews describing past research under the title: Paths to Discovery,
  • novel and proven laboratory experiments that have both skill-building and discovery-based characteristics,
  • reviews of relevant textbooks, software, and websites,
  • descriptions of software for educational use, and
  • descriptions of multimedia materials such as tutorials on various aspects of biochemistry and molecular biology.

The journal is published bimonthly by John Wiley & Sons for the International Union of Biochemistry and Molecular Biology (IUBMB). All articles are freely available after a 2-year hold. Four years of BAMBED articles (2002– 2005) are already freely available at the website (www. Soon we will add PDFs of back issues from 2000 and 2001.

One topic that has received increasing attention over the years is protein structure and its relationship to function. At one time a subject for graduate and post-doctoral study, now even high school students are exposed to the amazing field of protein structure. BAMBED has been an important tool in helping educators expand their ability to teach this important subject as more and more information has become available. Dissemination and use of this information has been made possible by the concomitant growth in the power of computers and computer software to allow visualization of these structures. In the 1960s and 1970s, students of protein structure built physical models of the few proteins for which structures were available, and molecular artists like Irving Geis drew 2D representations of these models. Now students visualize these structures on laptop computers using data from the RCSB PDB and freely-available software programs, or even directly from web browsers. One of BAMBED’s roles has been to help educators learn and teach the use of these visualization techniques, both in the classroom and in the laboratory. Since the year 2000, when we became co-editors-in-chief of BAMBED, many articles on this subject have been published. We urge the users of the RCSB PDB to share their educational techniques and programs by submitting manuscripts to BAMBED. Instructions to authors can be found at

Here are SOME EXAMPLES of papers on structural biochemistry that have recently been published in BAMBED. Most are available online for free. We hope that reading their titles will entice you to read further at BAMBED’s website, to submit your own education scholarship, and to subscribe. The papers are listed in chronological order:

David C. Richardson and Jane S. Richardson (2002) Teaching molecular 3D literacy. BAMBED 30: 21–26.

Brian White, Stella Kim, Katerina Sherman, and Nicole Weber (2002) Evaluation of molecular visualization software for teaching protein structure: Differing outcomes from lecture and lab. BAMBED 30:130–136.

Duane W. Sears (2002) Using inquiry-based exercises and interactive visuals to teach protein structure/function relationships. BAMBED 30: 208.

Kyle R. Willian (2002) Using 3D imaging of proteins: Examples of class activities and subsequent assessments. BAMBED 30: 209–210.

David W. Honey and James R. Cox (2003) Lesson plan for protein exploration in a large biochemistry class. BAMBED 31: 356–362.

W. Theodore Lee (2004) An interactive introduction to protein structure. BAMBED 32: 170–172.

Jacqueline R. Roberts, Eric Hagedorn, Paul Dillenburg, Michael Patrick, and Timothy Herman (2005) Physical models enhance molecular 3D literacy in an introductory biochemistry course. BAMBED 33: 105–110.

Sayan Mukherjee, Soumya De, Zhumur Ghosh, and Swagata Dasgupta (2005) A docking interaction study of the effect of critical mutations in ribonuclease a on protein-ligand binding. BAMBED 33: 335–343.

Konrad J. Schφnborn and Trevor R. Anderson (2006) The importance of visual literacy in the education of biochemists. BAMBED 34: 94–102.

Angel Herraez (2006) Biomolecules in the computer: Jmol to the rescue. BAMBED 34: 255–261.

Steven Bottomley, David Chandler, Eleanor Morgan, and Erik Helmerhorst (2006) jAMVLE, A new integrated molecular visualization learning environment. BAMBED 34: 343–349.

Laura Grell, Christopher Parkin, Len Slatest, and Paul A. Craig (2006) EZ-Viz, a tool for simplifying molecular viewing in PyMOL. BAMBED 34: 402–407.

Urmi Roy and Linda A. Luck (2007) Molecular modeling of estrogen receptor using molecular operating environment. BAMBED 35: 238–243.

Sandra K. Grunwald and Katherine J. Krueger (2008) Improvement of student understanding of how kinetic data facilitates the determination of amino acid catalytic function through an alkaline phosphatase structure/mechanism bioinformatics exercise. BAMBED 36: 9–15.

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