Chapter 43. GPU Computing for Protein Structure Prediction
Paulius MicikeviciusArmstrong Atlantic State University
Introduction
Determining protein 3D structure is one of the greatest challenges in computational biology. Nuclear magnetic resonance (NMR) spectroscopy is the second most popular method (after X-ray crystallography) for structure prediction. Given a molecule, NMR experiments provide upper and lower bounds on the interatomic distances. If all distances are known exactly, Cartesian coordinates for each atom can be easily computed. However, only a fraction (often fewer than 10 percent) of all distance bounds are obtained by NMR experiments (unknown upper and lower bounds are set to the molecule’s diameter and the diameter of a hydrogen ...
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