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Professor Ted Baker of Auckland University has been awarded the Rutherford Medal.
The professor, of the university's structural biology research group, received the country's most distinguished science award from Science and Technology Minister Steve Maharey in Auckland last night.
Professor Baker was the first person outside Europe or America to complete a protein structure.
"By looking at the structure of proteins we cannot only figure out how they work but can also develop new drugs and therapies, or even apply them in biotechnology," said the 64-year-old.
"All of the HIV drugs were designed by finding out the structure of the important protein of the virus and finding out how to block its activity and this whole process gives us the opportunity to design important drugs against specific diseases."
Professor Baker's work with x-ray crystallography was a first in New Zealand and enabled scientists to see these molecules.
"It's like going into a dark room and turning on the light. Suddenly you can see what you're dealing with and you can use your imagination to see how you can use it," Professor Baker said.
His research into the kiwifruit protein actinidin was later used by researchers in San Francisco to design anti-malarial drugs.
