Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
Proteins. 2011 Jun;79(6):1923-9. doi: 10.1002/prot.23015. Epub 2011 Apr 19.
Multibody potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Our goal was to combine long range multibody potentials and short range potentials to improve recognition of native structure among misfolded decoys. We optimized the weights for four-body nonsequential, four-body sequential, and short range potentials to obtain optimal model ranking results for threading and have compared these data against results obtained with other potentials (26 different coarse-grained potentials from the Potentials 'R'Us web server have been used). Our optimized multibody potentials outperform all other contact potentials in the recognition of the native structure among decoys, both for models from homology template-based modeling and from template-free modeling in CASP8 decoy sets. We have compared the results obtained for this optimized coarse-grained potentials, where each residue is represented by a single point, with results obtained by using the DFIRE potential, which takes into account atomic level information of proteins. We found that for all proteins larger than 80 amino acids our optimized coarse-grained potentials yield results comparable to those obtained with the atomic DFIRE potential.
多体势最近引起了广泛关注，因为它们考虑了与残基堆积有关的三维相互作用，并捕捉了蛋白质结构中这些相互作用的协同性。我们的目标是结合长程多体势和短程势，以提高错误折叠诱饵中天然结构的识别能力。我们优化了非顺序四体、顺序四体和短程势的权重，以获得最佳的排序结果，并将这些数据与其他势（来自 Potentials 'R'Us 网络服务器的 26 种不同的粗粒化势）的结果进行了比较。在识别同源模板建模和无模板建模的 CASP8 诱饵集中的天然结构时，我们优化的多体势在识别天然结构方面优于所有其他接触势。我们比较了这种优化的粗粒化势（其中每个残基用一个点表示）和 DFIRE 势（考虑蛋白质的原子水平信息）的结果。我们发现，对于所有大于 80 个氨基酸的蛋白质，我们优化的粗粒化势的结果与原子 DFIRE 势的结果相当。
