David Baker (born October 6, 1962 in Seattle, Washington) is an American biochemist and computational biologist who studies methods to predict the three-dimensional structures of proteins. He is a Professor of Biochemistry at the University of Washington, where he is the principal investigator of the 30+ member Baker laboratory. He is a Howard Hughes Medical Institute investigator, and as of April 2006, also a member of the United States National Academy of Sciences.

The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended to a distributed computing project called Rosetta@Home. The project aims to produce structural models for protein complexes as well as individual polypeptide chains. The Baker group participates regularly and is recognized for expertise in the CASP structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol.

Members of the Baker group are also active in the field of protein design; they are recognized as the first group to have designed a protein, known as Top7, with an entirely novel fold.