Annual Report 2011 - Center for Advanced Biotechnology and ...

Dr. Chenghua Shao
Research Associate
Dr. Lihua Tan
Research Associate
Dr. Yi-Ping Tao
Research Associate
Dr. Huanwang
Yang
Research Associate
Christine Zardecki
Research Associate
Dr. Marina
Zhuravleva
Research Associate
Kar Lun Chun
Research Assistant
Maria Voigt
Research Assistant
descriptions (annotations) from biological databases, as well as structural
genomics protein target information, experimental protocols, and the ability to
order available DNA clones. Text searches will find technology reports and
publications that were created by the PSI’s high-throughput research efforts, as
well as the monthly features and highlights from the website. Web tools that aid
in bench top research, such as protein construct design, are also available. This
information can enable scientists by providing everything that is known about a
protein sequence, including any experimental successes or failures, thus
streamlining their own research efforts.
The SBKB group also developed two entirely new resources for the Structural
Genomics community. First, a new experimental data tracking resource,
TargetTrack (sbkb.org/tt/), was created that merged two existing (and mostly
redundant) and expanding to support new types of high-throughput and
biological research. Second, a “Metrics” resource was created to track the
progress of the whole PSI program.
The Unified Data Resource for Cryo Electron Microscopy
The PDB archives large biological assemblies determined by cryo-electron
microscopy (cryoEM), a maturing methodology in structural biology that
bridges the gap between cell biology and the experimental techniques of X-ray
crystallography and NMR. In addition to 3D density maps, cryoEM experiments
often yield fitted coordinate models. Through an NIH/NIGMS-funded
collaboration, a joint EM map and model deposition tool has been developed.
The unified resource for deposition and retrieval network for cryoEM map,
model, and associated metadata is available at EMDataBank.org. This work
has been carried out in collaboration with the RCSB PDB at Rutgers, PDBe, and
the National Center for Macromolecular Imaging at Baylor College of Medicine.
Publications:
Dutta, S., Zardecki, C., Goodsell, D.S., and Berman, H.M. Promoting a
Structural View of Biology for Varied Audiences: An Overview of RCSB PDB
Resources and Experiences. Journal of Applied Crystallography. 2010 43:
1224-1229.
Lawson, C.L., Baker, M.L., Best, C., Bi, C., Dougherty, M., Feng, P., van
Ginkel, G., Devkota, B., Lagerstedt, I., Ludtke, S.J., Newman, R.H., Oldfield,
T.J., Rees, I., Sahni, G., Sala, R., Velankar, S., Warren, J., Westbrook, J.D.,
Henrick, K., Kleywegt, G.J., Berman, H.M., Chiu, W. EMDataBank.org:
unified data resource for CryoEM. Nucleic Acids Res. 2011 39: D456-D464.
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