Video: Shoichet, channeling William F. Buckley, offers a vigorous defense of docking and high-throughput screening for the graduate student retreat (interviewed by Emily Crawford, channeling Steven Colbert).
Podcast: Shoichet, in a public interview, tries desperately to sound less confused than he actually is.
Recent reviews, book chapters, and papers:
I am working on dock method development and performing large-scale docking to cool targets. My goal is to obtain a faculty position at a university were I plan to continue DOCK development and perform research focused on drug discovery and improving therapeutics. For more information about me visit my webpage.
Shuo Gu graduated from Hong Kong University of Science and Technology, where he studied protein-ligand interaction using molecular dynamics simulations. He is currently a postdoc in Shoichet lab, working on deorphanization of G protein-coupled receptors, part of the Illuminating The Druggable Genome.
Signal transduction is one of the most essential biological processes in all living organisms. G protein-coupled receptors (GPCRs) constitute the largest and most diverse family of cell surface receptors in the human genome, responsible for communicating messages between the cell's external and internal environments. A primary goal of my research is to integrate advancements in both our understanding of GPCR structure and in structure-based docking techniques, to realize the potential in targeting novel GPCR binding sites for drug discovery, as well as applying these techniques for exploring the functions of orphan GPCRs.
Purchasable chemical space is growing rapidly. We are docking these ever increasing databases. I am exploring what happens to docking when we go to larger and larger databases. I am also working on developing analysis tools for the large-scale docking.
My work in lab focuses on the use of protein crystallography and enzymology to test predictions emerging from large scale docking against AmpC beta-lactamase. Docking screens will also be used for new compound discovery against biologically relevant target like GPCR.
My work aims to incorporate receptor desolvation, the displacement of solvent from the binding site upon ligand binding, into the DOCK scoring function, a term which is currently neglected. This new term relies on continuum electrostatics, a quick method that represents the solvent as a homogeneous high dielectric medium. I will experimentally test ligands predicted from this new scoring function using binding assays and X-ray crystallography in a model cavity.
I am developing efficient computational docking pipelines for covalent inhibitor design. Now I have a special interest in designing lysine covalent probes by combine a variety of computational and experimental methods. My ultimate goal is to design covalent drugs for traditionally undruggable targets.
I am a joint graduate student in the Shoichet and Manglik Labs in the Pharmaceutical Sciences and Pharmacogenomics PhD program at UCSF. My background is in synthetic organic chemistry and natural product chemoenzymatic synthesis. I received my bachelor of science from Saint Mary's College of Califonia, and subsequently participated in the NIH PREP at Case Western Reserve University before matriculating at UCSF. I am interested in the pharmacology and structural biology of GPCR-mediated nociception. My work involves structure based design of novel analgesics targeting G-protein coupled receptors.
I am working on methods development in molecular docking including the incorporation of water energies, and calculation of relative binding free energy with higher levels of theory. I will then apply the methods to predict new ligands in both model systems and G Protein-coupled receptors (GPCRs).