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Dr. Michael K. Gilson

Computer-Aided Drug Design and Drug Discovery Informatics

Michael K. Gilson

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


(858) 822-0622


Research Summary: Supercomputing and Scientific Data to Accelerate Drug Discovery

Computer simulations of the molecules of life are now emerging as powerful tools for the design of new medications for a wide range of diseases, including cancer, heart disease, and Alzheimer’s. My lab is working to accelerate drug discovery by improving the realism, speed and accuracy of these fundamental simulations. We also created BindingDB, the first openly accessible database of medicinal research data, and we continue to expand and improve this resource in order to support drug discovery efforts worldwide.

One current project involves confronting calculations with matched experimental data to rigorously evaluate and improve the accuracy and speed of the simulations. In a parallel effort, we are using simulations to study the structure of water at the surfaces of biomolecules and learning how to take advantage of this structure in the design of new drugs to bind and disable disease-related proteins. We also are collaborating in the design of novel materials and catalysts for applications in energy production and pharmaceuticals. And we are partnering with pharmaceutical companies to make critical datasets available to drive the invention of new methods in computer-aided drug discovery. 

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:

Detur Prize (1978); John Harvard Scholarship (1978,1979); Tau Beta Pi Engineering Award (1981); Alfred Steiner Award (1987); Associated Medical Schools Award (1987); Louis Gibofsky Memorial Prize (1989); 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. 

Leadership Experience:

Co-Director UCSD Center for Drug Discovery Innovation 2013-present. Co-Founder, VeraChem LLC (2000-present). Scientific Advisory Board, Dart Neurosciences, 2013-present. Chair, NIH MSFD study section (2007-2008). Co-Organizer, SAMPL3 and SAMPL4 community prediction exercises, 2011, 2013. Organizer, Keystone Symposium on Computer-Aided Drug Design (2010). Vice-Chair, Faculty Senate, University of Maryland Biotechnology Institute (2008-2009). Editorial Advisory Boards: J. Med. Chem., Biopolymers, etc. 

Key Contributions to Pharmaceutical Sciences

  • Elucidated statistical thermodynamics of drug action
  • Contributed to 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 Recent Publications (from >120 peer-reviewed articles)

  • Nicola G et al. (2012). Public domain databases for medicinal chemistry. J. Med. Chem. 55:6987-7002
  • Pereira AR et al. (2012). The carmaphycins: new proteasome inhibitors exhibiting an alpha,beta- epoxyketone warhead from a marine cyanobacterium. ChemBioChem 13:810-817 (Was C-5)
  • Fenley AT et al. (2012). Entropy-enthalpy transduction due to conformational shifts can obscure the forces driving protein-ligand binding. Proc. Nat. Acad. Sci. USA, 109:20006-20011
  • Muddana HS et al (2014). Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J. Comput.-Aided Molec. Des. 10.1007/s10822- 014-9726-2
  • Nguyen,C. et al. (2014). Thermodynamics of water in an enzyme active site: grid-based hydration analysis of Coagulation Factor Xa. J. Chem. Theory Comput., 10:2769, 2014.
  • Fenley, A. et al. (2014). Bridging calorimetry and simulation through precise calculations of cucurbituril- guest binding enthalpies. J. Chem. Theory Comput. 10:4069-4078
  • Blum, A.P et al. (2014). Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J. Am. Chem. Soc.136:15422-37