Lab Members


Short Biosketch

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:

  • Shoichet BK. No free energy lunch. Nat Biotechnol 25 (10), 1109-10 (2007). [Pubmed | DOI | Download PDF]
  • Shoichet BK. Screening in a spirit haunted world. Drug Discov Today 11 (13-14), 607-15 (2006). [Pubmed | DOI | Download PDF]
  • Shoichet BK. Interpreting Steep Dose-Response Curves in Early Inhibitor Discovery. J Med Chem 49 (25), 7274-7277 (2006). [Pubmed | DOI | Download PDF]
  • Shoichet BK. Virtual Screening of Chemical Libraries (Review). Nature 432, 40-43 (2004). [Pubmed | DOI | PDF]
  • JJ Irwin & BK Shoichet.  Docking Screens for Novel Ligands Conferring New Biology. J. Med. Chem. 59, 4103-4120 (2016). [Pubmed | DOI | Download PDF]
  • BL Roth, JJ Irwin, BK Shoichet, Discovery of new GPCR ligands to illuminate new biology.  Nature Chemical Biology 13, 1143-1151 (2017). [Pubmed | DOI | Download PDF]


Trent Balius, Ph.D
Postdoc

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.

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Publications :


  • Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. PNAS 114 (33), E6839-E684 (2017). [Pubmed | DOI]
  • Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Homologous ligands accommodated by discrete conformations of a buried cavity. PNAS 112 (16), 5039-5044 (2015). [Pubmed | DOI | Download PDF]


Shou Gu,
Postdoc

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.

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Parnian Lak, PharmD PhD
Lab Manager

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Anat Levit, Ph.D
Postdoc

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.

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Publications :

  • Wang S, Che T, Levit A, Shoichet BK, Wacker D, Roth BL. Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone. Nature 555 (7695), 269 (2018). [Pubmed | DOI | PDB 6CM4]
  • Wacker D, Wang S, McCorvy JD, Betz RM, Venkatakrishnan AJ, Levit A, Lansu K, Schools ZL, Che T, Nichols DE, Shoichet BK, Dror RO, Roth BL. Crystal Structure of an LSD-Bound Human Serotonin Receptor. Cell 168 (3), 377-389 (2017). [Pubmed | DOI | F1000 | Newsweek | Scientific American | Nature NEWS | PDB 5TVN]
  • Wang S, Wacker W, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science 358 (6361), 381-386 (2017). [DOI | UCSF News | PDB 5WIU | PDB 5WIV]
  • Manglik A, Lin H, Aryal DK, McCorvy JD, Dengler D, Corder G, Levit A, Kling RC, Bernat V, Hübner H, Huang XP, Sassano MF, Giguère PM, Löber S, Da Duan, Scherrer G, Kobilka BK, Gmeiner P, Roth BL, Shoichet BK. Structure-based discovery of opioid analgesics with reduced side effects. Nature 537, 185-190 (2016). [Pubmed | DOI | BioCentury | Download PDF]


Jiankun Lyu, Ph.D
Postdoc

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.

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Publications :

  • Weiss, DR, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK. Selectivity Challenges in Docking Screens for GPCR Targets and Anti-Targets. J Med Chem , (2018). [Pubmed | DOI]
  • Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ. Ultra-large library docking for discovering new chemotypes. Nature. 2019 Feb; 566(7743):224-229. [Pubmed | DOI]


Matthew O'Meara, Ph.D
Postdoc

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Publications :

  • Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. Prediction of enzymatic pathways by integrative pathway mapping. Elife 7, e31097 (2018). [Pubmed | DOI]
  • O'Meara MJ, Ballouz S, Shoichet BK, Gillis J. Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS ONE 11 (7), e0160098 (2016). [Pubmed | DOI | Download PDF]


Isha Singh, Ph.D
Postdoc

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.

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Reed Stein, PSPG
Graduate Student

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.

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Publications :

  • Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. PNAS 114 (33), E6839-E684 (2017). [Pubmed | DOI]


Xiaobo Wan, Ph.D
Postdoctoral Fellow

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. 

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Chase Webb, PSPG
Graduate Student

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. 

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Ying Yang, Ph.D
Postdoc

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).

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