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.^[1] He also serves as an editor of the journal Structure.

Šali received his Bachelor of Science degree in chemistry from University of Ljubljana, 1987; his Ph.D. in Molecular Biophysics from Birkbeck College,^[2] University of London, 1991 (working with Tom Blundell); and did postdoctoral work at Harvard University (working with Martin Karplus).

Sali joined the faculty of the Rockefeller University in 1995, following his postdoctoral research at Harvard University. 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.^[4]

Sali contributes greatly to structural biology by developing and applying computational methods for structural modeling and analysis of proteins. The two most often used programs developed by his research group include "MODELLER" for comparative protein structure modeling and "IMP" for integrative structure determination.

As of January 2022, Šali published approximately 400 papers,^[5] which were cited approximately 89,000 times per Google Scholar. His Hirsch-index is 132 (i.e., 132 publication have been cited at least 132 times).

In 2018, Šali was elected member of the National Academy of Sciences in recognition of his contributions to biophysics and computational biology.^[6]