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

Winter 2010
Number 44

Home | Newsletter Archive | PDF Version
Message from the RCSB PDB
Data Deposition
2009 Statistics
Data Deposition Resources
Data Query, Reporting and Access
2009 Statistics
New and Improved Web Services for Accessing PDB Data
wwPDB FTP Advisory Notice
New Website Features
Outreach and Education
Poster Prize Awarded at ECM
Recent and Upcoming Meetings
Education Corner
IJsbrand M. Kramer, Ph.D.: A Search for Best Methods to Illustrate Complex Information

Outreach and Education

Poster Prize Awarded at ECM

Yonka Yuzugullu

Poster Prize Awarded at ECM Yonca Yuzugullu was awarded the RCSB PDB Poster Prize at the 25th European Crystallographic Meeting (August 16-21, 2009; Istanbul, Turkey) for Crystallization of bifunctional catalase-phenol oxidase (CATPO) from Scytalidium thermophilum. Yonca Yuzugullu, Chi Trinh, Arwen R. Pearson, Mark A. Smith, Simon Phillips, Ufuk Bakir, Michael J. McPherson, Zumrut B. Ogel (Middle East Technical University, Turkey).

Many thanks to Elspeth Garman (University of Oxford) and Joel Sussman (Weizmann Institute of Science) for judging the posters, and to Andreas Roodt (University of the Free State, South Africa) for organizing the judging.




Recent and Upcoming Meetings

Science teachers at the NJSC learned how to build tRNA?from a cloverleaf representation into a 3D paper model?through a presentation by Shuchismita Dutta.

At the New Jersey Science Convention (NJSC; October 13-14; Somerset, NJ), science teachers visiting the RCSB PDB booth learned about the structures in the PDB archive and the RCSB PDB materials available for use in their classrooms. Many teachers also created tRNA structures out of paper during a presentation by Shuchismita Dutta.

From December 5-9, the RCSB PDB exhibited at the 49th Annual Meeting of the American Society for Cell Biology in San Diego, CA alongside the PSI Structural Genomics Knowledgebase (PSI SGKB). David Goodsell, author of the Molecule of the Month, discussed Visual Representation from Atoms to Cells: New Work from the Machinery of Life as part of a session on Exploring Cell Biology at the Frontier of 3D Visualization.

John Westbrook chaired a session on Ligands in the PDB at the eCheminfo Community of Practice Meeting on Advances in Drug Discovery and Development (October 13-16; Philadelphia, PA). The session, a continuation of a session chaired by Marc Nicklaus (National Institutes of Health) at the 2008 eCheminfo meeting, explored issues related to interpreting ligand structural data in the PDB.

Presentations included Ligand Pocket Detection in Biological Assemblies (Howard Feldman, Chemical Computing Group), Conformer Generation: Finding and Learning from Failures (Paul Hawkins, OpenEye Scientific Software), The PDB and Antibiotic Peptide Sequence-like Compounds (Kim Henrick, PDBe), Thoughts about Ligand-Structure Validation (Gerard J. Kleywegt, PDBe), electronic Ligand Builder and Optimisation Workbench (eLBOW): A tool for Ligand Coordinate and Restraint Generation (Nigel W. Moriarty, Lawrence Berkeley National Laboratory), Ligand Energies Calculated Quantum-Chemically in Vacuum and Solvent Model (Marc Nicklaus), Iridium: Marginally Less Bad than the Rest (Gregory L Warren, OpenEye Scientific Software, Inc.), Enabling the World of Internet Based Chemistry Through ChemSpider (Valery Tkachenko, Royal Society of Chemistry), and Mitotic Kinesin Eg5 Inhibitors Generation By Computational MED-Portion Based Drug Design at PDB Scale (François Delfaud, MEDIT).

At Cold Spring Harbor Laboratory?s course X-Ray Methods In Structural Biology (October 12-27), John Westbrook presented PDB Tools for Depositors.

Helen Berman described the process of Annotation of Carbohydrates in the PDB at the NIH?s Workshop on Leveraging Glycan Array Screens with Biological, Computational and Structural Data (October 22-23, Bethesda, MD).

Phil Bourne presented The Changing Landscape of Scholarly Communication as it Relates to the Biosciences at the 19th Keck Center Annual Research Conference on Computation in Biology: from Gene to Neuron (October 29-30, Rice University) and The Evolution of Protein Structure and Function as Studied through Structural Bioinformatics at the 18th Annual Buffalo-Hamilton-Toronto Symposium (November 6, McMaster University)

Peter Rose demonstrated the resources of the RCSB PDB to visitors to the ACS CHEM EXPO, held in Balboa Park, San Diego.The San Diego Section of the American Chemical Society (ACS) celebrated National Chemistry Week by holding CHEM EXPO in Balboa Park (November 1). At the RCSB PDB booth, middle and high school students, plus parents and teachers, learned about drugs and proteins using a variety of materials and displays.

Future meetings include the Keystone Symposia Frontiers of NMR in Biology (January 8-13, 2010; Breckenridge, CO) the Biophysical Society Annual Meeting (February 20-24; San Franci­sco), and the National Science Teacher Association?s Annual Meeting (March 18-21; Philadelphia, PA). The RCSB PDB will also be participating in the San Diego Science Festival and Rutgers Day this spring. Details will be announced at

  Participating RCSB Members: Rutgers • SDSC/SKAGGS/UCSD
E-mail: • Web: • FTP:
The RCSB PDB is a member of the wwPDB (
©2009 RCSB PDB