Michael Levitt, a British-US citizen of Stanford University; US-Austrian Martin Karplus of Strasbourg University; and US-Israeli Arieh Warshel of the University of Southern California will share the prize.
The trio devised computer simulations to understand chemical processes.
In doing so, they laid the foundations for new kinds of pharmaceuticals.
Today, scientists routinely use modelling to understand how different biological molecules interact, to probe the mechanisms of disease and to design novel drugs.
The silent partner in this prize is the incredible development in computer power
Michael Levitt, Stanford University
"The Nobel Laureates in Chemistry 2013 have made it possible to map the mysterious ways of chemistry by using computers," said the Royal Swedish Academy of Sciences.
"Today the computer is just as important a tool for chemists as the test tube.
"Detailed knowledge of chemical processes makes it possible to optimise catalysts, drugs and solar cells."
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