Dr. Michael K. Gilson

Supercomputing and Scientific Data to Accelerate Drug Discovery

Michael K. Gilson, M.D., Ph.D.

Skaggs School of Pharmacy and Pharmaceutical Sciences Chair in Computer-Aided Drug Design
UCSD Center for Drug Discovery Innovation

Prounouns:  he|him|his

(858) 822-0622
Research Summary

Computer simulations of the molecules of life are powerful tools for the design of new medications for a wide range of diseases. My lab accelerates drug discovery by improving the realism, speed, and accuracy of these fundamental simulations through methods development and software development and sharing. We also run BindingDB, an open database of measured protein-small molecule binding data over 2 million data for over 1 million compounds, and we are actively engaged in molecular design and synthesis for drug discovery projects relating to cancer and anesthesia.


Academic Achievements


A.B. Bioengineering Magna cum Laude, (1981) Harvard College; Ph.D. in Biochemistry and Molecular Biophysics (1988) Columbia University; M.D. (1989) Columbia University College of Physicians and Surgeons. 

Awards and Honors:

Howard Hughes Medical Institute Physician Research Fellowship (1991-94). Distinguished Lecture in Computational and Mathematical Biology, University of California, Irvine (2014). Endowed Chair in Computer-Aided Drug Design, UC San Diego, 2010- present. 5th Annual Kollman Lectureship, UC San Francisco, 2016

Leadership Experience:

Executive Committee, UC Drug Discovery Consortium, 2018- present. Co-Director UCSD Center for Drug Discovery Innovation 2013-present. Co-Founder, VeraChem LLC (2000-present). Chair, NIH MSFD study section (2007-2008). Member of Editorial Advisory Boards; e.g., J. Med. Chem., J. Chem. Inf. Mod. 

Key Contributions
  • Statistical thermodynamics of protein-drug binding as a basis for binding affinity calculations
  • Structure-based development of mutation-resistant HIV-protease inhibitors
  • Invented the Mining Minima technology for computer-aided drug design
  • Founded BindingDB, a public, web-accessible medicinal chemistry database
Selected Publications
  • Ben-Shalom, I.; Lin, C.; Radak, B.; Sherman, W.; Gilson, M. Fast Equilibration of Water between Buried Sites and Bulk by MD with Parallel Monte Carlo Water Moves on GPUs. 2021. https://doi.org/10.33774/chemrxiv-2021-mgpfv-v2.
  • Heinzelmann, G.; Gilson, M. K. Automation of Absolute Protein-Ligand Binding Free Energy Calculations for Docking Refinement and Compound Evaluation. Sci. Rep. 2021, 11 (1), 1116. https://doi.org/10.1038/s41598-020-80769-1.
  • Qiu, Y.; Smith, D. G. A.; Boothroyd, S.; Jang, H.; Hahn, D. F.; Wagner, J.; Bannan, C. C.; Gokey, T.; Lim, V. T.; Stern, C. D.; Rizzi, A.; Tjanaka, B.; Tresadern, G.; Lucas, X.; Shirts, M. R.; Gilson, M. K.; Chodera, J. D.; Bayly, C. I.; Mobley, D. L.; Wang, L.-P. Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field. J. Chem. Theory Comput. 2021, 17 (10), 6262–6280. https://doi.org/10.1021/acs.jctc.1c00571.
  • Ricci-Lopez, J.; Aguila, S. A.; Gilson, M. K.; Brizuela, C. A. Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. J. Chem. Inf. Model. 2021. https://doi.org/10.1021/acs.jcim.1c00511.
  • Amber 2021 molecular simulation software. https://tinyurl.com/amber2021-citation