UCSF department of Pharmaceutical Chemistry

Research Facilities

Biomolecular Resource Center (BRC)

The Biomolecular Resource Center (BRC) is a University of California at San Francisco full-service biotechnology core facility. We provide the campus research community with a full range of protein and nucleic acid services, including synthesis, sequencing, purification, and analysis. With intensive use of state-of-the-art instrumentation, the BRC synthesizes and analyzes over 30,000 samples a year for over 240 principal investigators. Most of these investigators are located at UCSF's Parnassus, Mission Bay and Mt. Zion campuses, VAMC, SFGH, other universities, and private companies.

The BRC is a non-profit, non-subsidized facility and operates on a cost-for-service basis. As required by federal guidelines, our charges equal our actual costs. The facility is governed by a Board of Overseers comprised of members from departments and research units that make extensive use of the facility.

Computer Graphics Laboratory (CGL)

The Computer Graphics Laboratory was established in 1969 as a National Research Resource of the National Institutes of Health, providing access to state-of-the-art computer graphics hardware and software for research on biomolecular structures and interactions. The laboratory is used extensively not only within the department and campus, but by visitors from around the world. Equipment includes Compaq and Hewlett-Packard computers for numerical and symbolic computing, as well as Silicon Graphics high performance interactive three-dimensional color graphics systems for visualizations of complex structures. Hewlett-Packard and NeXT workstations are used for program and interface development and documentation. All systems are interconnected via a high speed local area network, and fast access is also provided to remote computing facilities such as the San Diego Supercomputer Center. Computers employ the UNIX operating system (various 'flavors'), Linux and Windows. Software developed in the laboratory, particularly the molecular display program MidasPlus and Chimera, are widely distributed to other sites and are in use in applications including molecular modeling, drug design and protein engineering.

The Nuclear Magnetic Resonance Laboratory (NMR)

The Nuclear Magnetic Resonance Laboratory in Genentech Hall is equipped with state of the art high-field NMR spectrometers for chemistry and studies of macromolecular structure. For routine proton-heteronuclear and 2D NMR experiments, a 400 MHz Varian Inova spectrometer is available in room GH-S102. In room GH-S106, two Varian 600 MHz spectrometers and a Brunker 500 MHz spectrometer are available for high-resolution studies of macromolecules including solution structure determination of proteins, nucleic acids, and their complexes. The spectrometers have complete 2D and 3D NMR capabilities (including inverse detection, triple resonance, pulsed field gradients and tailored excitation) permitting use of virtually all modern pulse sequences for solution NMR experiments. In addition, room GH-S106 contains a newly installed state-of-the-art Brunker 800MHz spectrometer. The Brunker 500 MHz and 800 MHz spectrometers are equipped with Cryoprobes, and one of the Varian Inova 600 systems has a Coldprobe. Multidimensional NMR data are transferred to a dedicated data processing system composed of a server, several Silicon Graphics workstations, and a Linux based cluster for off-line data processing and analysis.

More information regarding the NMR lab, including scheduling, can be found at the following website: http://picasso.ucsf.edu. This website also enables others to access NMR software developed here such as SPARKY, CORMA, MARDIGRAS, CHIRANO, and other programs useful for structure refinement.

Contact information:

http://picasso.ucsf.edu/New/contact.html

The Mass Spectrometry Facility (MSF)

The National Bio-Organic, Biomedical Mass Spectrometry Resource, supported by the NIH National Center for Research Resources, provides both scientific and technical expertise and state-of-the-art high-performance, tandem mass spectrometric instrumentation. The facility is equipped with a VG-70S, a Kratos Concept IIHH and an Autospec-orthogonal time of flight tandem instrument. These mass spectrometers can operate in electron-bombardment, positive and negative ion chemical-ionization, liquid matrix secondary ion sputtering, electrospray and matrix laser ionization modes. The VG-70S mass spectrometer interfaces with conventional and capillary gas chromatographs and is computer-controlled for selected monitoring and quantitative measurements. The facility also enjoys important new tools including capillary HPLC electrospray mass spectrometry and matrix-assisted laser desorption time of flight mass spectrometry, both of prime importance in studies of structural biology.

Molecular Design Institute (MDI)

The Molecular Design Institute provides a multidisciplinary organization for research groups working on macromolecular structure and molecular design and is an administrative home for large scale collaborative projects aimed at infectious disease, cancer and parasitology including NIH Program Project Grants in "Structural Biology and Targeted Drug Design for AIDS" and "Proteases in Cancer".

The Sequence Analysis and Consulting Service (SACS)

The Sequence Analysis and Consulting Service provide DNA and protein sequence analysis software, databases and consulting services for over 105 subscribing labs doing molecular biology at the University of California San Francisco.

Campus Resources

The available computational resources are among the world's best in computational chemistry and biology. Hardware platforms include high performance workstations from Compaq, Hewlett Packard, IBM, Silicon Graphics, Sun Microsystems and numerous Linux and Mac stations (including clusters). Computers and workstations on campus are connected to campus-wide local area network, which in turn is connected via high speed microwave link to the Internet. Access to remote computer facilities, such as the NFS-sponsored supercomputer centers, is also available via this Internet link. Access to extensive literature databases is available through such systems as MEDLINE and the University's MELVYL system. An on-line journal system provides desktop access to full text and graphics images for a limited, but growing, number of journals. A central aspect of the computer resources is the Computer Graphic Laboratory within the Department of Pharmaceutical Chemistry, which has been both developing state-of-the-art software for molecular modeling and design as well as providing access to high performance interactive graphics since 1969.