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Supercomputer Sets Protein-Folding Record
Nicros writes with this snippet from Nature News:
"A specially designed supercomputer named Anton has simulated changes in a protein's three-dimensional structure over a period of a millisecond — a time-scale more than a hundred-fold greater than the previous record. ... The simulations revealed how the proteins changed as they folded, unfolded and folded again. 'The agreement with experimental data is amazing,' says Chandra Verma, a computational structural biologist at the Bioinformatics Institute of the Agency for Science, Technology and Research in Singapore. Simulating the basic pancreatic trypsin inhibitor over the course of a millisecond took Anton about 100 days — roughly as long as computers spent toiling over previous simulations that only spanned 10 microseconds."
The best way is to just compare them to the actual structure which is known from x-ray crystallography and NMR studies. They could do isotopic replacement studies to get ideas about which hydrogrens or nitrogens or carbons were kinetically involved in the folding process and see whether the same atoms were important in the simulation. If they're the same it could just be a coincidence, or it could be an indication that the folding itself is accurate on the computer, not just the final structure. This is truly amazing, but we've still got a long ways to go. MOAR COMPUTERS PRZ!