UCSF QB3
1700 4th Street, Byers Hall
San Francisco, CA 94143-2540
(CA 94158 for courier delivery)
301 (computational lab)
309 (experimental lab)
308 E (Tanja Kortemme's office)
Principal Investigator
Tanja Kortemme
My main scientific interests range from the details of the physical interactions between atoms and molecules to the architecture and evolution of interaction networks in complex biological systems.
Vordiplom (BS)
Chemistry,
Physical Chemistry
University of Hannover, Germany
Diplom (MSc)
Biophysics
Stanford University / University of Hannover
Dr.rer.nat (Ph.D.)
Biochemistry
EMBL Heidelberg / University of Hannover
Postdoctoral work in computational and structural biology at EMBL Heidelberg and the Howard Hughes Medical Institute, University of Washington, Seattle
Postdoctoral Researchers
Mariana Babor
I enjoy travelling. A lot!
I am interested in understanding and modulating mechanisms that lead to protein cross-reactivity -- in particular those that result from protein flexibility. To address these questions, I will combine computational and experimental strategies.
Licenciatura
Biology
University of Buenos Aires, Argentina
Master of Science
Bioinformatics
Weizmann Institute of Sceince, Israel
Ph.D.
Bioinformatics
Weizmann Institute of Sceince, Israel
Sen Liu
Nice bridge.
I am interested in the design of protein structures and functions. To do this, I will use experimental and computational approaches. At present, I'm working on the design of orthogonal interaction pairs of the critical GTPases and their natural partners involved in cell migration. We hope the success on these designs can be used to control cell behaviors, and used in synthetic biology studies.
Bachelor of Science
Biotechnology
China Three Gorges University
Ph.D.
Physical Chemistry
Peking University, China
Specialist
Cristina Melero
During my free time, I enjoy hiking, biking and other outdoors activties. I also love big white dogs, as you can see (dog not shown).
I apply a combination of computational and experimental approaches to protein-protein interactions in PDZ domain containing proteins. My work will help to elucidate the contributions of specific residues to both affinity and specificity in PDZ-ligand interactions. More generally, we hope to understand how PDZ domain containing proteins help organize multimeric complexes involved in essential cellular processes.
Bachelor of Science
Physical Chemistry
Complutense University, Madrid
Graduate Students
Matt Eames
I play for keeps.
I'm investigating the molecular evolution of protein domains and networks. I'm also developing experimental techniques to probe the asymmetric evolution of genes.
Previous Work: Co-Owner - FM Mowers, VA; Driver - Red Cross, VA; Drive-Thru Cashier - Taco Bell, VA; Waiter - Luciano's, VA; Indexer - Indexing Partners, VA; Fire Fighter - National Park Service, CA; Bartender - The Yorkshire Grey, UK; Plumber/Technician - Eltron Research, CO; Chief Technical Officer - Lucid Dimensions, CO
Bachelor of Science
Physics
University of Virginia
Dan Mandell
That's right, Billy.
My theoretical work concerns the treatment of proteins as conformational ensembles to relax the fixed-backbone assumption during protein design. Currently I am developing a procedure derived from robotic kinematics to generate multiple backbone conformations for protein interfaces to broaden the sequence space sampled during interface redesign. On the practical side, I am applying these methods for two purposes: (1) to produce "adaptor" proteins to mediate interactions between aggregation prone mutants of disease related proteins and chaperones to facilitate their folding, (2) to design highly specific cell surface-binding proteins to interfere with signaling cascades exploited during cancer metastasis and angiogenesis.
Bachelor of Science
Symbolic Systems
Stanford University
Master of Science
Artificial Intelligence
University of Edinburgh, UK
Elisabeth Humphris
I heart proteins.
I am working on extending our lab's current computational methods for the prediction and design of protein-protein interactions by developing a "multi-state" design algorithm, which would allow multiple selective pressures to simultaneously be present during the computational optimization process.
This project would model the integration of various selective pressures on cellular signaling proteins which have evolved a specific amino acid sequence for both maximizing desired properties (such as fold stability and correct binding of desired signaling molecules) while simultaneously minimizing undesirable properties (such as unwanted cross-talk with incorrect binding partners). If successful, "multi-state" design methodologies should give us 1) an improved understanding of a per-residue contribution to binding specificity and 2) improvement in our ability to experimentally engineering "designer" proteins with altered binding properties. Once developed in relation to protein-protein specificity, the "multi-state" design methodology proposed here could easily be extended to determine the optimal amino acid sequence for proteins which could adopt several structural conformations or perform several functions.
Bachelor of Arts
Natural Sciences (Biology/Mathematics)
New College of Florida
Rich Oberdorf
I am but a man, hanging off the edge of an enormous protein.
Although there is a strong global relationship between mean protein abundance and abundance noise, there is also important structure in the degree to which individual proteins deviate from this global correspondence that suggests selection for high or low noise in the expression of specific proteins. Noisy gene expression could impair cell function by disrupting cell signaling and regulation. Conversely, stochasticity in gene expression could be beneficially exploited to enhance cellular diversity or be required for successful transitioning between states. While some consequences of cellular variability on organism fitness have been suggested, direct tests have been limited. My work seeks to directly test the effects of varying expression noise levels by establishing systematic methods for manipulating expression variation while preserving mean expression and measuring the fitness effects that result from such perturbations.
Bachelor of Science
Physics and Mathematics
Brandeis University
Colin Smith
My other scientific interest is studying self-induced hypothermia while swimming in San Francisco Bay.
My research centers around the functionally relevant loop motions of proteins in their native state. I am developing and evaluating models which capture and efficiently sample those motions in all-atom simulations. Using Monte Carlo and other techniques, I am interested
in improving our ability to accurately predict the free energies of transitions on the microsecond time scale. Towards that end, I aim to develop model systems for experimentally testing and refining our techniques for prediction/design of directed flexibility. Longer term, I want to engineer a local allosteric switch into a protein which is not currently allosterically regulated.
Bachelor of Arts
Biology and Computer Science
New York University
Ryan Ritterson
I would start a company that would build a hydrogen infrastructure so we can move our economy off petroleum.
I am principally interested in the computational reengineering and
redesign of biological objects to both answer difficult scientific
questions as well as solve interesting problems in both biological
systems and larger abiotic contexts. Currently, I am seeking ways to
pry out new knowledge about the relationship between cadherin-
mediated adhesion and cell to cell signaling, with the hope of both
learning more about how the two processes are interrelated and
perhaps discovering novel ways of controlling them.
Bachelor of Science
Computational Engineering Science
UC Berkeley
Noah Ollikainen
I can't find my glasses!
I'm currently developing efficient algorithms for protein interface design. Specifically, I am working on a new deterministic approach that can handle multiple constraints and still converge to the global minimum energy conformation in a short amount of time. I plan to apply this approach to engineer proteins with altered interaction specificities.
Bachelor of Science
Bioinformatics
UCSD
Software Engineer
Florian Lauck
Surprisingly, I prefer a lager to a stout.
I'm working on computational methods for the prediction of protein interfaces,
particularly in order to make them available to the public.
Bachelor of Science
Bioinformatics
Saarland University, Germany
Master of Science
Bioinformatics
Saarland University, Germany
Past Rotation Students
Geoff Rollins, Biophysics, Winter, 2009
Rocco Varela, BMI, Winter, 2009
Roxana Ordonez, BMI, Summer, 2008
Elaine Kirshke, Biophysics, Winter, 2008
Charles Kehoe, BMI, Winter, 2008
Jaline Gerardin, Biophysics, Fall, 2007
Alvin Tamsir, Tetrad, Spring, 2007
Sheel Dandekar, Biophysics, Spring 2006
Reid Williams, Biophysics, Fall 2006
Dan Gray, CCB, Fall 2006
Michael Hicks, PSPG, Winter 2005
Chris McClendon, Biophysics, Fall 2005
Ian Harwood, Biophysics, Spring 2005
Kareen Riviere, PSPG, Winter 2005
Mike Keiser, BMI, Fall 2004
Lab Alumni
Greg Kapp, PhD - Scientist, Omniox Inc.
Greg Friedland, PhD - Postdoc, Joint Bioenergy Institute & UC Berkeley
Catherine Shi - UCSD
Anthony Linares - MD/PhD student UCLA
David Lomelin - Graduate Student, Risch lab, UCSF
Loren Baugh, PhD - Postdoc, University of Washington
