Structural Bioinformatics and Systems Pharmacology

Elizabeth Winzeler

Faculty Status
Active
Title
Professor
Email
ewinzeler@ucsd.edu
Phone
(858) 822-3339
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
My laboratory uses big data approaches to solve problems in global health. The lab also offers training in cheminformatics and chemical genomics.

Hannah Carter

Faculty Status
Active
Title
Assistant Professor of Medicine
Email
hkcarter@ucsd.edu
Phone
(858) 822-4706
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Structural Bioinformatics, Systems Biology, Machine Learning, Cancer, Personalized Medicine and Genetic Variation

Nathan E. Lewis

Faculty Status
Active
Title
Associate Professor
Email
n4lewis@ucsd.edu
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Systems biology approaches for integration of disparate data types to study diseases involving metabolism, glycobiology, and to guide cell engineering for drug development.

Roger Tsien

Faculty Status
Inactive
Title
Professor
Email
rtsien@ucsd.edu
Phone
(858) 534-4891
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Molecular Engineering, Synaptic Plasticity, CAPKs

Susan Taylor

Faculty Status
Active
Title
Professor
Email
staylor@ucsd.edu
Phone
(858) 534-3677
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Relationship of CAPK Structure to Function
Lab Description

cAMP-dependent protein kinase (PKA) is ubiquitous in every mammalian cell with the PKA signaling network regulating processes as diverse as memory, differentiation, development, the cell cycle, and circadian rhythms. One of our goals, in addition to elucidating structures of the PKA subunits, is to map the PKA proteome as it relates to PKA signaling. The PKA interaction network consists not only of the PKA regulatory and catalytic subunits as well as the GPCRs, G-Proteins, cyclases, and phosphodiesterases, as well as PKA substrates but also the scaffold proteins (A Kinase Anchoring Proteins: AKAPs) that target PKA to specific sites in the cell. We are interested, in particular to map PKA that is targeted to organelles such as the mitochondria. A second goal is to map the activity of PKA in live cells using FRET PKA activity reporters that are targeted to specific sites such as the plasma membrane, the mitochondria, or the nucleus.

Andrew McCulloch

Faculty Status
Active
Title
Professor
Email
amcculloch@ucsd.edu
Phone
(858) 534-2547
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Mathematical Modeling of Heart Cells and Tissue

Andrew McCammon

Faculty Status
Active
Title
Professor
Email
jmccammon@ucsd.edu
Phone
(858) 534-2905
Track(s)
Bioinformatics and Systems Biology
Brief Research Description
Enzymes and Ligand Binding
Lab Description

The McCammon group conducts a very wide range of research activities, from the deeply biological (studies of protein and nucleic acid targets for drugs for infectious diseases, studies of protein kinase regulation, etc.) to the development of mathematical and physical methods for simulating biological processes (development of methods for solving partial differential equations, exploring the role of hydrodynamic interactions in protein-protein association, etc.). All of this work involves the use of computers; we do no experimental work in the traditional sense, but we have extensive collaborations with experimental labs at UCSD, The Scripps Research Institute, The Salk Institute, and elsewhere. A more complete perspective can best be obtained by visiting the McCammon group website (http://mccammon.ucsd.edu/). We welcome undergraduate research participants when space allows, as described in http://mccammon.ucsd.edu/UGResOp.html

Michael Gilson

Faculty Status
Active
Title
Professor
Email
mgilson@ucsd.edu
Phone
(858) 822-0622
Track(s)
Bioinformatics and Systems Biology
Department
Brief Research Description
Computer-aided drug discovery
Lab Description

We work on many aspects of molecular mechanism, modeling and design.  Our core interests are in the physical chemistry and algorithms underpinning computer-aided drug design methods, but we also have much wider interests, such as simple model receptors for studying molecular recognition; how molecule motors work; chemical informatics and its interface with bioinformatics; how membranes work; and synthetic catalysts and nanoparticles.