Lab members
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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. Education
Postdoctoral work Computational and structural biology at EMBL Heidelberg and the Howard Hughes Medical Institute, University of Washington, Seattle. Tanja's publications |
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Postdoctoral scholars
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Lin Liu
I work on development and application of computational methods for the prediction of protein structures and the design of protein interactions. In particular, I apply robotics-based algorithms for modeling of protein conformations and for multi-constraint protein design, developed in the Kortemme lab, and apply these methodologies to experimental model system. I also test predictions experimentally on the CypA system. Education
Lin's publications |
I am a super fan of Raymond Lam ^_^
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Tina Perica
I am interested in studying the genotype-to-phenotype relationships by using the knowledge of protein structure and biophysics. I aim to do that by testing the quantitative effects of designed perturbations on the genetic interactions. Sir Henry Wellcome Postdoctoral Fellow Education
Tina's publications |
#Post-Dog
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Anum Azam Glasgow
I am interested in self-assembling systems and protein complexes. I am working on developing methods to design and experimentally test chemically inducible dimerization systems to produce versatile protein biosensors and improve our understanding of protein-ligand interfaces. Education
Anum's publications |
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graduate students
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Pradeep Bandaru
I am interested in (1) coupling large-scale mutagenesis and physics-based protein design to understand the mechanism of allosteric regulation in mammalian signaling proteins, (2) understanding how signaling pathways are robust to perturbations in their protein components, and (3) defining the evolutionary principles that led to the design of these signaling pathways. I am also advised by Professor John Kuriyan at UC Berkeley. Education
Pradeep's publications |
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Kyle Barlow
I am interested in taking a humid approach to protein design. I am working on integrating new algorithms into the Rosetta framework to assist in the design process. I hope to engineer proteins that are relevant for human health or biofuel synthesis. ARCS graduate fellow Education
Kyle's Publications |
Coffee and tea are a grad student's best friend
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Cody Krivacic
I am interested in understanding how best to apply our computational tools to protein engineering challenges. I am currently working on a computational method that re-positions amino acids of interest by manipulating the protein backbone and testing my designs experimentally. The ability to precisely define side-chain positions in protein binding sites will enable the engineering of proteins with altered specificity. Education
Cody's publications |
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Kale Kundert
I am interested in computationally engineering the extent to which different conformations of a protein are present at equilibrium. This technology has many applications, but a prime example is the design of an artificial switch protein. The activity of the switch could be tuned by changing the equilibrium between the "on" and "off" conformations. Another good example is the modulation of binding between two partners that interact via conformational selection. I am working both to develop algorithms that can predict protein conformational equilibria and to pursue the two example applications described above. Education
Kale's publications |
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Amanda Loshbaugh
I am interested in developing protein tools for molecular biology. Currently I am experimentally characterizing biosensors that detect small molecules in vivo. My thesis work will aim to develop transcription factors and other tools that exhibit digital behavior for application in cell circuits. Education
Amanda's publications |
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James Lucas
I am interested in utilizing molecular biology techniques to investigate protein structure-function relationships as well as developing Rosetta to engineer tools for synthetic biology. I am currently developing a general protocol for designing analyte-induced dimerization domains coupled with split-protein reporters as reliable in vivo biosensors. NSF Graduate Fellow Education
James's publications |
Derp.
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Chris Mathy
My interests generally center around the ability of organisms to finely control system-wide behavior by tuning of protein structures and interfaces. My current work uses computational kinetic models to examine the effect of mutations on a conserved protein switch. Education
Chris's publications |
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XingJie Pan
I am interested in understanding and designing biological systems in a bottom-up approach, since a physical system is not truly understood until we can calculate its behavior from physics laws. Currently I am working on developing algorithms for reshaping protein functional sites. Education
Xingjie's publications |
Whereof one cannot speak, thereof one must be silent.
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Samuel Thompson
Protein function is often described in terms of a static structure and a small number of functionally important residues, but the less than realistic representation of proteins as single states could be undermining our ability to model function. By modeling functional proteins as multi-constraint ensembles in Rosetta, I am probing the connections between functional sequence space and the balance between the energies of multiple functional states. NSF Graduate Fellow Education
Samuel's publications |
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staff
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