We are part of:
Department of Bioengineering and Therapeutic Sciences
California Institute for Quantitative Biosciences (QB3)
Integrative Program in Quantitative Biology
Graduate Group in Biophysics
Graduate Program in Bioinformatics
Graduate Program in Chemistry and Chemical Biology (CCB)
Synthetic Biology Engineering and Research Center (SynBERC)
We are located at:
1700 4th Street, Byers Hall 308E
UCSF MC 2530
San Francisco, CA 94143-2530
(CA 94158 for courier delivery)
301 (computational lab)
309 (experimental lab)
308E (Tanja Kortemme's office)

Principal Investigator

 Tanja Kortemme Tanja
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.

See Tanja's publications.

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 Scholars

 Daniel Hoersch Daniel This is no figure caption.
Groups II chaperonins are molecular machines employing the energy of ATP hydrolysis to mediate protein folding in eukaryotes and archea via a still largely enigmatic mechanism. I am currently working on a project using an engineering approach towards elucidating chaperonin mechanism with two interrelated goals: First, to test functional hypotheses derived from recent high-resolution structures of group II chaperonins in multiple conformations; and second, to convert a model chaperonin, the biochemically tractable archeal Mm-cpn, from an ATP- to a light-driven machine.

See Daniel's publications.

DFG postdoctoral fellow

Vordiplom (BS)    Physics   Ludwig-Maximilians-Universitaet, Germany
Diplom (MSc)    Physics   Freie Universitaet Berlin, Germany
Dr.rer.nat. (Ph.D.)    Physics   Freie Universitaet Berlin, Germany
Postdoctoral work in molecular biophysics at Freie Universitaet Berlin

 Amelie Stein Amelie Usually I'm more colorful.
I study protein interactions to elucidate which molecular and cellular factors determine the high specificity observed in such interactions, currently focusing on yeast Gsp1 and bacterial two-component signal transduction systems.

See Amelie's publications.

EMBO postdoctoral fellow

Bachelor of Science    Computer Science / Bioinformatics   University of Tübingen, Germany
Master of Science    Computer Science / Bioinformatics   University of Tübingen, Germany and UNC Chapel Hill, NC, USA
Ph.D.    Bioinformatics / Biomedicine   IRB Barcelona and Universitat Pompeu Fabra, Barcelona, Spain
Postdoctoral work in structural and computational biology at IRB Barcelona

 Roland Pache Roland In my free time I practice Aikido and explore the world of photography.
During my PhD, I developed a powerful novel method for the alignment of protein interaction networks, called NetAligner. This method allows to easily compare networks of arbitrary topology, including protein complexes, pathways and whole interactomes, with a wide range of possible applications. For my postdoc, I moved from the field of Network Biology over to Structural Biology, basically changing from a 2D perspective on studying protein interactions to a 3D one. I am now mostly interested in protein loop modeling by robotics-inspired conformational sampling, as well as in the design of protein interactions and molecular biosensors.

See Roland's publications.

Bachelor of Science    Computer Science (Bioinformatics)   University of Tübingen, Germany
Master of Science    Computer Science (Bioinformatics)   University of Tübingen, Germany
Ph.D.    Biomedicine (Bioinformatics)   University of Barcelona, Spain

 Yao-ming Huang Yao-ming
My research surrounds the relationship between protein sequences and protein structures. In particular I study the usage of HMMSTR structure prediction in improving sequence alignment, the engineering of green fluorescent protein as a potential peptide biosensor, and the development of computational protein design algorithms.

See Yao-ming's publications.

Bachelor of Science    Medical Technology   National Taiwan University, Taipei, Taiwan
Master of Science    Molecular Biology / Biochemistry   National Taiwan University, Taipei, Taiwan
Ph.D.    Structural Biology / Bioinformatics   Rensselaer Polytechnic Institute, New York, USA
Postdoctoral research in structural and computational biology at Rensselaer Polytechnic Institute

 Lin Liu Lin I am a super fan of Raymond Lam ^_^
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.

See Lin's publications.

Bachelor of Science    Biological Science   University of Science and Technology of China, Hefei, China
Ph.D.    Molecular Biophysics and Structural Biology   University of Pittsurgh, Pittsburgh, PA, USA

 Tina Perica Tina This is my usual amount of colour.
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.

See Tina's publications.

Sir Henry Wellcome Postdoctoral Fellow

Bachelor of Science    Molecular Biology   Zagreb University, Croatia
Ph.D.    Molecular Biology   Cambridge University, UK

 Noah Ollikainen Noah 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.

See Noah's publications.

NSF graduate fellow

Bachelor of Science    Bioinformatics   UCSD


 Ryan Ritterson Ryan I stole Noah's glasses!
I am interested in the reengineering and redesign of biological objects to solve problems for which nature has yet no answer. Previously, I worked to re-engineer cell-cell adhesion proteins so they could be controlled with light. Currently, I work on characterizing protein-based small molecule biosensors, to allow nature to detect and respond to things in ways they currently cannot.

See Ryan's publications.

Bachelor of Science    Computational Engineering Science   UC Berkeley
Ph.D.    Biophysics   UC San Francisco

Graduate Students

 Laurens Kraal Laurens I want to 3D print my thesis
My academic interests comprise synthetic biology, microbial ecology, microbial interactions and genome organization. Using comparative genomics on the plethora of microbial genomes currently available, my computational research aims to identify functional clusters and protein interaction networks that are specific to either phylogeny or ecology. Experimentally, I hope to validate my findings using synthetic biology and whole genome engineering.

See Laurens's publications.

ARCS graduate fellow

Bachelor of Arts    Theoretical Philosophy   University of Groningen
Bachelor of Science    Molecular Biology   University of Groningen
Master of Science    Biomedical Sciences   Utrecht University

 Kyle Barlow Kyle Coffee and tea are a grad student's best friend
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.

See Kyle's publications.

ARCS graduate fellow

Bachelor of Arts    Molecular and Cell Biology   UC Berkeley

 Kale Kundert Kale
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.

Bachelor of Science    Chemical Biology   UC Berkeley

 Amanda Loshbaugh Amanda
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.

Bachelor of Arts    Biochemistry   Oberlin College

 Pradeep Bandaru Pradeep
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.

See Pradeep's publications.

Bachelor of Science    Applied Mathematics   Columbia University
Master of Arts    Biomedical Informatics   Columbia University

 Samuel Thompson Samuel 色って何だろう?
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 required states. I want to better understand how each state helps define the sequence space such that we can design non-evolutionary sequences that conform to all required states.

See Samuel's publications.

NSF Graduate Fellow

Bachelor of Science    Chemistry   Massachusetts Institute of Technology

Software Engineer

 Shane O'Connor Shane Have you tried turning it off and on again?
My interest is in using scripting to build frameworks around the scientific software used in the lab with the goal of allowing rapid-prototyping and development. My background includes work on garbage collection in a memory-managed scripting language. I maintain and update the Backrub webserver and take care of some IT administrative tasks.

See Shane's publications.

Bachelor of Arts    Information and Communications Technology   Trinity College Dublin, Ireland
Ph.D.    Computer Science   Trinity College Dublin, Ireland
Postdoctoral work in commercial scripting engines for console-based videogame development at Trinity College Dublin, Ireland

Lab Administrator

 Joslyn Polzien Joslyn Usually, I'm less colorful.
In addition to my B.A. I studied basic sciences at San Francisco State University, and am excited to be part of the Kortemme lab team after nine years doing administrative work in non-profit education.

Bachelor of Arts    Japan Studies & East Asian Studies   Macalester College

Past Rotation Students

Justin Biel, Biophysics, Winter 2014
Kevin Hartman, Bioinformatics, Winter 2014
Rebecca Davidson, Biophysics, Winter 2013
Russell Goodman, Biophysics, Winter 2012
Lawrence Uricchio, Bioengineering, Winter 2012
Leo Gendelev, Biophysics, Summer 2012
Alec Nielsen, Biophysics, Winter 2011
David Mavor, Biophysics, Summer 2011
Joel Karpiak, CCB, Winter 2010
Geoff Rollins, Biophysics, Winter 2009
Rocco Varela, BMI, Winter 2009
Ian Vaughn, Biophysics, Fall 2009
Elaine Kirshke, Biophysics, Winter 2008
Charles Kehoe, BMI, Winter 2008
Roxana Ordonez, BMI, Summer 2008
Jaline Gerardin, Biophysics, Fall 2007
Alvin Tamsir, Tetrad, Spring 2007
Reid Williams, Biophysics, Fall 2006
Dan Gray, CCB, Fall 2006
Sheel Dandekar, Biophysics, Spring 2006
Michael Hicks, PSPG, Winter 2005
Kareen Riviere, PSPG, Winter 2005
Chris McClendon, Biophysics, Fall 2005
Ian Harwood, Biophysics, Spring 2005
Mike Keiser, BMI, Fall 2004

Lab Alumni

Debbie Jeon, BS 2009-2013 MD Program, George Washington University
Cristina Melero, MSc 2004-2012 Scientist, Intrexon Inc.
Victor Ruiz, BS 2012 Graduate program, Yale
Ashley Custer 2010-2012 Graduate program, Boston University
Eyal Akiva, PhD 2010-2011 Postdoc, UCSF
Rich Oberdorf, PhD 2005-2011 Ab Initio Software Corporation
Colin Smith, PhD 2006-2011 Postdoc, Max Planck Institute Goettingen, Germany
Dan Mandell, PhD 2005-2011 Postdoc, Harvard University
Matt Eames, PhD 2005-2011 Postdoc, NYU
Sen Liu, PhD 2008-2010 Associate Professor, Three Gorges University, China
Florian Lauck, MSc 2008-2010 Specialist, UCSF
Michael Michalik 2009-2010 Graduate Program, University of Bonn, Germany
Thomas Bliska 2010 Undergraduate, Williams College
Aaron Nichols 2010 Undergraduate, UC Riverside
Elisabeth Humphris, PhD 2005-2009 Postdoc, Yale
Matt Chroust 2009 Dentistry Graduate Program, UCSF
Mariana Babor, PhD 2006-2009 University of Toronto
Greg Kapp, PhD 2004-2009 Scientist, Omniox Inc.
Greg Friedland, PhD 2004-2008 Postdoc, Joint Bioenergy Institute & UC Berkeley
Catherine Shi 2008 iPQB graduate program, UCSF
Anthony Linares 2006-2007 MD/PhD program, UCLA
David Lomelin 2004-2006 BMI graduate program, UCSF
Loren Baugh, PhD 2004-2005 Postdoc, University of Washington Seattle

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