Andrej Šali (born 1963, Kranj, Slovenia) is a computational structural biologist.

Since 2003, he has been Professor in the Department of Bioengineering and Therapeutic Sciences at University of California, San Francisco.

He is using computation grounded in the laws of physics and evolution to study the structure and function of proteins.

For example, he developed comparative protein structure modeling by satisfaction of spatial restraints, implemented in program MODELLER[3] and integrative structure determination of macromolecular assemblies, implemented in program IMP.

In 2018, Šali was elected member of the National Academy of Sciences in recognition of his contributions to biophysics and computational biology.