"The advantage that Mathematica provides is a breadth of techniques that are already implemented and can be connected with great fluidity. This encourages exploration and experimentation."

Form Determines Function in the World of Proteins

"Determining how to use the linear amino acid sequence of a protein to predict its structure is the most significant problem in computational biology," claims Robert Jones, director of computing at Darwin Molecular Corporation. A key component in scientists' investigation of protein structure at Darwin is Mathematica.

Researchers statistically analyze the sequence and known properties of a protein to derive constraints on how far apart certain amino acids must be in the structure. Using distance geometry methods, they work on finding a three-dimensional configuration consistent with their matrix of distance constraints.

"Mathematica is a ready toolkit of powerful mathematical functions that makes it easy to try new techniques," says researcher Matt Fitzgibbon. "The programming facilities allow us to rapidly prototype new ideas and make changes to the algorithms. And the notebooks simplify the development by recording our results for future analysis."

"Understanding protein structure helps us understand how proteins function," explains Fitzgibbon. And that understanding gives scientists insight that may lead to discoveries of new ways to fight viral infection, of methods of transporting therapeutics in the body, or of ways to curb autoimmune disease.

Key features of Mathematica used:

• Numeric--matrix functions (particularly eigenvector and eigenvalue), linear algebra functions
• Graphic--3D polylines to show derived structures
• Programming
• Notebook--"extremely useful for storing and annotating intermediate steps in algorithm development"