Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
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DOI：
10.1110/ps.0217002
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发表时间：
2002-11-01
期刊：
影响因子：
8
通讯作者：
Zhou, YQ
中科院分区：
文献类型：
--
作者：
Zhou, HY;Zhou, YQ
到目前为止开发的依赖于距离的结构衍生的电位都采用了一个参考状态，可以被表征为残基（原子）平均状态。在这里，我们建立了一个新的参考状态称为距离缩放，有限理想气体参考（DFIRE）状态。参考状态用于从分辨率小于2埃的10 - 11个非同源（小于30%同源性）蛋白质结构的数据库构建平均力的残基特异性全原子势。新的全原子势从32个多诱饵集合中识别出更多的天然蛋白质，并将平均Z分数提高了1.4个单位，比以前开发的两个残基特异性全原子知识为基础的势高。当仅使用骨架和C-β原子评分时，基于DFIRE的电位的性能虽然比全原子版本的性能差，但与先前开发的全原子水平上的电位的性能相当。此外，在三种基于知识的全原子势中，基于DFIRE的全原子势对895个突变体的稳定性提供了最准确的预测。与几个物理为基础的潜力进行了比较。
The distance-dependent structure-derived potentials developed so far all employed a reference state that can be characterized as a residue (atom)-averaged state. Here, we establish a new reference state called the distance-scaled, finite ideal-gas reference (DFIRE) state. The reference state is Used to construct a residue-specific all-atom potential of mean force from a database of 10 11 nonhomologous (less than 30% homology) protein structures with resolution less than 2 Angstrom. The new all-atom potential recognizes more native proteins from 32 multiple decoy sets, and raises an average Z-score by 1.4 units more than two previously developed, residue-specific, all-atom knowledge-based potentials. When only backbone and C-beta atoms are used in scoring, the performance of the DFIRE-based potential, although is worse than that of the all-atom version, is comparable to those of the previously developed potentials on the all-atom level. In addition, the DFIRE-based all-atom potential provides the most accurate prediction of the stabilities of 895 mutants among three knowledge-based all-atom potentials. Comparison with several physical-based potentials is made.