Former ME PhD student Jungkap Park and Professor Kazuhiro Saitou have set the new record for accuracy in the standard benchmarking suites for predicting protein structures.
In his PhD dissertation supervised by Professor Saitou, Park developed a new multibody statistical potential function to characterize tightly folded proteins by considering a chemical bond’s rotameric states, which previous work had not fully explored.
The new potential, dubbed ROTAS (short for rotamer-dependent atomic statistical potential), sheds light on the otherwise unknown correlation between the specificity of atomic interactions and bonds’ rotameric states. After being tested on the standard decoys for benchmarking protein structure prediction algorithms, they concluded that ROTAS predicts protein structures better than any existing potential functions. The results can be applied to improve qualities in protein design, mutation analysis, and docking simulation.
The results were published this past September in a research article entitled, “ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures,” in BMC Bioinformatics (http://www.biomedcentral.com/1471-2105/15/307/abstract).
Park is currently at the Pacific Northwest National Laboratory in Washington, where he investigates computational proteomics.