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

More documents

Recommendations

Info

Dr. Helen M. Berman Board of Governors Professor Department of Chemistry and Chemical Biology Interim Director Biological, Mathematical, and Physical Sciences Interfaces (BioMaPS), Director RCSB Protein Data Bank Director PSI Structural Biology Knowledgebase Rutgers University Dr. Martha Quesada Research Professor Dr. John Westbrook Research Professor Dr. Feng Zukang Research Professor Dr. Catherine Lawson Associate Research Professor Dr. Shuchismita Dutta Assistant Research Professor Dr. Monica Sekharan Assistant Research Professor Dr. Jasmine Young Assistant Research Professor Structural Biology and Bioinformatics Dr. Berman's research area is structural biology and bioinformatics, with a special focus on protein-nucleic acid interactions. She is the founder of the Nucleic Acid Database, a repository of information about the structures of nucleic acid-containing molecules; and is the co-founder and Director of the Protein Data Bank, the international repository of the structures of biological macromolecules. Professor Berman also leads the Protein Structure Initiative Structural Biology Knowledgebase. She is a Fellow of the American Association for the Advancement of Science and of the Biophysical Society, from which she received the Distinguished Service Award in 2000. A past president of the American Crystallographic Association, she is a recipient of the Buerger Award (2006) and a member of the inaugural class of ACA Fellows (2011). Dr. Berman received her A.B. in 1964 from Barnard College and a Ph.D. in 1967 from the University of Pittsburgh. She received the Department of Chemistry Alumni Award from the University of Pittsburgh in 2010. The Protein Data Bank The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) supports scientific research and education worldwide by providing an essential resource of information about biomolecular structures. The PDB archive is the single repository of information about the 3D structures of large biological molecules, primarily proteins and nucleic acids. Scientists from around the world submit their data about their experiments to the PDB, which is then processed and made freely available in the PDB archive. The RCSB PDB, which is based at Rutgers and the University of California, San Diego, manages the PDB archive as a member of the Worldwide PDB (wwPDB). The wwPDB organization (www.wwpdb.org) was formed to ensure that the PDB archive is and will be freely and publicly available to the global community. The wwPDB members (RCSB PDB, Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj), and the BioMagResBank (BMRB)) host deposition, processing, and distribution centers for PDB data and collaborate on a variety of projects and outreach efforts. As 'archive keeper' for the wwPDB, the RCSB PDB maintains the central repository of the PDB archive. The central activity of the wwPDB is the collection, validation, archiving and distribution of high quality structural data to the scientific community on a timely basis. The systems developed by the RCSB PDB are reliable and stable to meet the challenges of high data rates and complex structures. As of November 8, 2011, the PDB archive contains more than 77,000 entries. 47
In 2011, the wwPDB commemorated the PDB’s 40 th anniversary with a special symposium. The meeting was attended by 19 distinguished speakers, approximately 250 participants, and 93 poster presentations. 34 travel awards for early career scientists were made using funds raised by the wwPDB. More information about the meeting is available at http://meetings.cshl.edu/meetings/pdb40.shtml. The RCSB PDB’s website at www.pdb.org provides access to the PDB FTP archive as well as tools that help users search, analyze and visualize PDB structural data. In 2010, the RCSB PDB website had more than 5.6 million visits by users in 218 countries. On average, the website has more than 196,000 unique visitors each month. Additionally, 160,713,233 data files were downloaded from the FTP server in 2010. The website provides access to a relational database that integrates PDB data with related information from external sources (such as journal abstracts, functional descriptors, sequence annotations, structure annotations, and taxonomy). Users can search for structures using simple searches (PDB ID, keyword, sequence, or author) and complex queries. PDB-101 is a unique view of the RCSB PDB that packages together the resources of interest to teachers, students, and the general public. Major topics include Molecule of the Month columns, a top-down exploration from high-level functional categories to PDB structures called Structural View of Biology, and related Educational Resources and materials. The RCSB PDB group at Rutgers is involved with undergraduate and graduate education, and supports local K12 education with programs such as the protein modeling event at the New Jersey Science Olympiad, and K12 education throughout the world with online resources. Structural Genomics and the PSI Structural Biology Knowledgebase With the overarching goal of creating new knowledge about the interrelationships of sequence, structure, and function, the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB, sbkb.org) is a free online resource that captures and highlights the structural and technical advances made by the PSI structural genomics efforts for use by the broader biological community. This information is integrated with publicly available biological information so that it can enable a better understanding of living systems and disease. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase also provides a research library, highlights focused on new research advances and technical tips, the latest science news, and an events calendar to present a broader view of structural genomics and structural biology. Searches of the SBKB by sequence or PDB ID will yield a list of related protein structures from the Protein Data Bank, theoretical 3D models, associated Li Chen Research Associate Dr. Buvna Coimbatore- Narayanan Research Associate Dr. Luigi DiCostanzo Research Associate Dr. Margaret Gabanyi Research Associate Guanghua Gao Research Associate Saheli Ghosh Research Associate Dr. Sutapa Ghosh Research Associate Vladimir Guranovic Research Associate Dr. Brian Hudson Research Associate Aamir Jadoon Research Associate David Micallef Research Associate Dr. Ezra Peisach Research Associate Dr. Irina Persikova Research Associate Nomi Rom Research Associate Raul Sala Research Associate Raship Shah Research Associate 48
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 50 and 51: Dr. Chenghua Shao Research Associat
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
Page 58 and 59: Zhao, L., Zhao, K., Hurst, R., Slat
Page 60 and 61: Acton, T.B., Xiao, R., Anderson, S.
Page 62 and 63: Kryshtafovych, A., Bartual, S.G., B
Page 64 and 65: properties by lowering susceptibili
Page 66 and 67: Dr. Ann M. Stock Associate Director
Page 68 and 69: Publications: Barbieri, C.M., Mack,
Page 70 and 71: Lectures and Seminars 69
Page 72 and 73: CABM RETREAT, June 30, 2011 Cook Ca
Page 75 and 76: 25 th Anniversary CABM Symposium Fr
Page 77 and 78: Edery Lab Joseph Albistur George Gh
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
Page 85 and 86: Former CABM Scientific Advisory Boa
Page 87 and 88: Fiscal Information 86
Page 89 and 90: Anderson, Stephen Rutgers CABM Gran
Page 91 and 92: Leukemia & Lymphoma Society BFL-1 a
Page 93 and 94: Total Award Start - End FY 2011 Dir
Page 95 and 96: Department of Defense Tumor suppres
Page 97 and 98: Total Award Start - End FY 2011 Dir

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

Create successful ePaper yourself

Delete template?

Save as template?