Under the deal, Schrödinger could receive up to $120m, which includes preclinical milestones.
Computer aided design (CAD) plays a major role in nearly all industries ranging from airplane design to movie making but it is not widely recognized as a truly enabling technology in the field of drug discovery.
Additionally, a new enterprise informatics system to facilitate real-time collaboration between computational designers and medicinal chemists, will serve as the communications and project management platform for researchers across the two companies.
Schrödinger president Ramy Farid said: "Our mission is to transform drug discovery through computational technology, and we will continue to commit the resources necessary to develop compelling scientific solutions.
Sanofi president Global R&D Elias Zerhouni said: "Collaborating with Schrödinger is an effective way for Sanofi to gain access to first rate computational design resources.
"In the interest of perpetual innovation, we are constantly looking at cutting-edge technologies to advance our research."
In recent years, Schrödinger has made a number of key scientific breakthroughs in the areas of protein and ligand structure determination and potency prediction which could have a transformative impact on the discovery of drugs.