why is it so hard to determine proteins tertiary stucture using computers? We can know what smaller molecules look like in 3D why not proteins?
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Determining the three-dimensional structure of a biological macromolecule by crystallography involves a number of clearly defined steps. First, crystals of suitable size and diffraction properties must be prepared. Next, x-ray diffraction data must be collected for these crystals and also, typically, for a number of heavy atom derivatives of the crystals. These data can then be assembled to obtain an electron density map using a computational process that resembles the action of the lens in a microscope. This map must then be fitted with a polypeptide chain of the appropriate amino acid sequence. Because the map is of less-than-atomic resolution and also contains errors in the phase determination, the investigator must have considerable skill to obtain the best fit. The resulting protein model must then be refined to remove the errors present in the map as much as possible as well as those errors introduced by the fitting process.
Computers play an essential role in most of these steps. Even the analyses of the first protein crystal structure, myoglobin, could not have been accomplished without the use of the EDSACII in Cambridge (Kendrew, 1960). At present, modern crystallography depends completely on heavy computer use, and this dependence will certainly increase steadily in the future. In the four mathematical procedures required to solve a structure using protein crystallography—data processing, phase determination, map fitting, and refinement—new methods are continually appearing that depend on ready access to considerable computer power.
for more info: http://www.ncbi.nlm.nih.gov/books/NBK218560/