Automatically updated information about Matt’s publications can be found at the following websites:
Google Scholar
UCSF Profiles

A manually annotated (with links to commentaries, resources, etc.) list can be found on this website here

If you are interested in specific topics, you can select one of these:

Computer-aided drug design (including both docking and ADME prediction)

Enzyme function prediction (including specific applications to Isoprenoid synthases)

Our papers on various aspects of protein regulation, by post-translational modifications (including phosphorylation), pH, and allostery

Papers that use various computational methods:  Docking, molecular dynamics, Monte Carlo, or quantum mechanics

My earlier work on protein structure prediction (including for antibodies) and even earlier work in chemical physics.  There are also a few papers that don’t fit into any of the other categories, focusing on interesting aspects of biophysics such as electrostatics, diffusion, and protein dynamics.

Review or perspective papers, or those with Commentaries or F1000 reviews.  I also wrote a textbook a long time ago.