Pathways Bioinformatics & Biomolecular Center at the City College of New York

1. Pathways Bioinformatics & Biomolecular Center at the City College of New York Supported by the Howard Hughes Medical Institute Undergraduate Science Education Program and the National Science Foundation. Core Faculty: Dr. Yuying Gosser, Bioinformatics, Director Dr. Vivian Stojanoff, Synchrotron Crystallography Brookhaven Natinal Lab, Co-Director Dr. Peter Brass, Computer Science, Co-Director Dr. Shubha Govind Molecular Genetics, Co-Director Dr. David Calhoun Biochemistry Dr. David K.Gosser, Analytical Chemistry Marshak Science Building, Room 1102 Tel: 212/650-8870 Fax: 212/650-8339 Email: Pathways@sci.ccny.cuny.edu URL: http://deepspace9.sci.ccny.cuny.edu Pathways Bioinformatics & Biomolecular Center The mission of this Center is to provide a compelling pathway which empowers undergraduate students with information technology and biomolecular laboratory methods, and engages them in discovery research in the interdisciplinary fields of bioinformatics, molecular genetics and structural biology. The Center is equipped with: • Research Software: • Molecular Operating Environment (MOE) for homology modeling docking, structure display and analysis; • A suite of software, including Xplor/CNS, for protein/RNA structure calculation with data obtained from X-ray diffraction or NMR spectroscopy; • DNAStar for gene sequence analysis and primer design; • “R” package based software for microarray data analysis. • A modern facility for molecular genetics and DNA recombinant experiments, and protein expression and purification; • Facility for protein crystallization and access to BNL X6A beam line, and CCNY NMR facility. • A cluster of computers for computation in Bioinformatics and Computational Biology. New courses that engage students in discovery research in biomolecular science and engineering: Summer Bioinformatics Workshop: A four week intensive workshop with topics that include: Bioinformatics and Internet resources; the NCBI data model and GenBank database; sequence alignment; phylogenetic analysis; protein structure prediction, homology modeling and visualization; artistic presentation of protein structures and cell events, microRNA; statistical analysis of microarray gene expression data; computer programming and molecular graphics. Biomolecular Systems Course (Bio31612/Chem31212, Spring Semester): A laboratory-based course that introduces bioinformatics databases, computational software and modern experimental technologies in molecular genetics and structural biology. This course will focus on the structural basis of biomolecular sciences and ' in silico' experiments. The follow-up bench-top experiments in gene expression, protein purification and structure analysis using NMR and X-ray crystallography will be offered in a summer research course. d θ ( θ ) nλ = 2d sinθ Math Art, programming and molecular graphics (Sci 31401) This course introduces symmetry, geometric shape and symmetry with classical examples of visual art; Two general technologies in computer graphics: PostScript and Ray Tracing; visualization and molecular graphics. Howard Hughes Medical Institute Undergraduate Researchers Each year, the Center will designate undergraduates from the science and engineering disciplines as Undergraduate Researchers. These students will be supported to participate in the research of the Pathways Bioinformatics and Biomolecular Center, at associated medical institute laboratories, or in the participating faculty members’ laboratories Research Areas • Statistical analysis of microarray data and database programming • Computational screening of the function of conserved non-coding DNA • Visualization and analysis of protein and RNA structures, and structural characterization using x-ray crystallography and/or NMR spectroscopy • Enzyme-ligand interactions and in vitro screening of inhibitors. • Electrochemical analysis of biological redox systems.