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

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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. 49
Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlić, A., Quesada, M., Quinn, G.B., Westbrook, J.D., Young, J., Yukich, B., Zardecki, C., Berman, H.M., Bourne, P.E., The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011 39: D392-D401. Bluhm, W.F., Beran, B., Bi, C., Dimitropoulos, D., Prlić, A., Quinn, G.B., Rose, P.W., Shah, C., Yukich, B., Berman, H.M., Bourne, P.E., Quality Assurance for the Query and Distribution Systems of the RCSB Protein Data Bank. Database. 2011. Rose, P.W., Bluhm, W.F., Beran, B., Bi, C., Dimitropoulos, D., Goodsell, D.S., Prlić, A., Quinn, G.B., Yukich, B., Berman, H.M., Bourne, P.E. The RCSB Protein Data Bank: site functionality and bioinformatics use cases. NCI-Nature Pathway Interaction Database Bioinformatics Primer. 2011. Gabanyi, M.J., Adams, P.D., Arnold, K., Bordoli, L., Carter, L.G., Flippen- Anderson, J., Gifford, L., Haas, J., Kouranov, A., McLaughlin, W.A., Micallef, D.I., Minor, W., Shah, R., Schwede, T., Tao,YP.W., Westbrook, J.D., Zimmerman, M., Berman, H.M. The Structural Biology Knowledgebase: A portal to protein structures, sequences, functions, and methods. Journal of Structural and Functional Genomics 2011 12:45-54. Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Feng, Z., Goodsell, D.S., Prlic, A., Quinn, G., Rose, P., Westbrook, J., Yukich, B., Young, J., Zardecki, C., Berman, H.M. The Evolution of the RCSB Protein Data Bank Website. WIREs Computational Molecular Science. 2011. Berman, H.M. The Protein Data Bank: Evolution of a key resource in biology. Leadership in Science and Technology: A Reference Handbook (William Sims Bainbridge, editor) SAGE Publications, Inc., 2011. Kryshtafovych, A., Bartual, S., Bazan, J.F., Berman, H.M., Casteel, D., Christodoulou, E., Everett, J., Hausmann, J., Heidebrecht, T., Hills, T., Hui, R., Hunt, J., Jayaramanand, S., Joachimiak, A., Kennedy, M., Kim, C., Lingel, A., Michalska, K., Montelione, G., Otero, J., Perrakis, O., Pizarro,J., vanRaaij, M.J., Ramelot, T., Rousseau, F., Wernimont, A., Young, J., Schwede, T. Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction. PROTEINS: Structure, Function, and Bioinformatics, 2011 79: 6–20. 50
Page 1: CENTER FOR ADVANCED BIOTECHNOLOGY A
Page 4 and 5: Director’s Overview CABM—25 and
Page 6 and 7: of Health, National Science Foundat
Page 8 and 9: Cell & Developmental Biology Labora
Page 10 and 11: protein metabolism/activity, such t
Page 12 and 13: Dr. Céline Gélinas CABM Resident
Page 14 and 15: (CHINJ, CINJ and CABM) and Lauri Go
Page 16 and 17: Dr. Masayori Inouye CABM Resident F
Page 18 and 19: Xu, Z., Mirochnitchenko, O., Xu, C.
Page 20 and 21: Dr. Fang Liu CABM Resident Faculty
Page 22 and 23: Publications: Matsuura, I., Chiang,
Page 24 and 25: In the prior year, we have made con
Page 26 and 27: Dr. James Millonig CABM Resident Fa
Page 28 and 29: We have mapped 5 different vl modif
Page 30 and 31: Dr. Arnold Rabson Director Child He
Page 32 and 33: Publications: Zheng, X., Cui, X.X.,
Page 34 and 35: polymerase II, facilitating the sel
Page 36 and 37: Dr. Mengqing Xiang CABM Resident Fa
Page 38 and 39: neurons diminish while there is a s
Page 40 and 41: Laboratory Faculty Director Structu
Page 42 and 43: Human transcription factors are typ
Page 44 and 45: atomic detail and have yielded nume
Page 46 and 47: Figure from Das et al., 2011 showin
Page 48 and 49: Dr. Helen M. Berman Board of Govern
Page 52 and 53: Dr. Joseph Marcotrigiano CABM Resid
Page 54 and 55: The long-term goals of our studies
Page 56 and 57: s Publications: Singarapu, K.K., Mi
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Page 66 and 67: Dr. Ann M. Stock Associate Director
Page 68 and 69: Publications: Barbieri, C.M., Mack,
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Page 79 and 80: PATENTS P. Lobel, et al. “Methods
Page 81 and 82: Montelione, G.T., Ma, L. and Krug,
Page 83 and 84: Outside Academic Members Dr. Wayne
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Page 87 and 88: Fiscal Information 86
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Page 93 and 94: Total Award Start - End FY 2011 Dir
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