PRIMO: A Transferable Coarse-grained Force Field for Proteins.
PRIMO: A Transferable Coarse-grained Force Field for Proteins.
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DOI：
10.1021/ct400230y
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发表时间：
2013-08-13
影响因子：
5.5
通讯作者：
Feig M
中科院分区：
文献类型：
--
作者：
Kar P;Gopal SM;Cheng YM;Predeus A;Feig M
我们在这里描述了PRIMO（蛋白质中间模型）力场，这是一个基于物理的完全可转移的加性粗粒度势能函数，适用于多尺度模拟的全原子力场。能量函数由标准分子动力学能量项加氢键势项组成，主要基于CHARMM22/CMAP力场自下而上参数化。溶剂通过广义玻恩模型隐式处理。键的相互作用是谐波电位或基于距离的样条插值电位。这些电位是在基于CHARMM22/CMAP力场的二肽全原子分子动力学（MD）模拟的基础上定义的。通过将不同构象的构象自由能与CHARMM全原子结果相匹配来调整非键参数。PRIMO旨在为所有氨基酸提供具有CMAP校正项的主链（φ /ψ）和侧链（χ1）的构象分布的正确描述。基于新的CHARMM C36 CMAP，对PRIMO中的CMAP电位进行了优化。将优化后的力场应用于36-155个氨基酸的几种蛋白质的分子动力学模拟，结果表明，平均结构与相应晶体结构的均方根偏差在1.80 ~ 4.03 Å之间。PRIMO被证明可以将几个小肽从扩展构象折叠成它们的天然结构。这些结果表明PRIMO力场适用于水溶液中蛋白质结构的研究、结构预测以及小肽的从头折叠。
We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36–155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides.
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影响因子：
2.9
作者：
Cheon, Mookyung;Chang, Iksoo;Hall, Carol K.
通讯作者：
Hall, Carol K.
影响因子：
3.3
作者：
Brini, Emiliano;Marcon, Valentina;van der Vegt, Nico F. A.
通讯作者：
van der Vegt, Nico F. A.
影响因子：
5.5
作者：
Best, Robert B.;Zhu, Xiao;Shim, Jihyun;Lopes, Pedro E. M.;Mittal, Jeetain;Feig, Michael;MacKerell, Alexander D., Jr.
通讯作者：
MacKerell, Alexander D., Jr.
DOI：
10.1109/tcbb.2011.141
发表时间：
2012
期刊：
IEEE/ACM transactions on computational biology and bioinformatics
影响因子：
--
作者：
Cheng YM;Gopal SM;Law SM;Feig M
通讯作者：
Feig M
DOI：
10.1016/j.str.2008.03.013
发表时间：
2008-07
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Ding F;Tsao D;Nie H;Dokholyan NV
通讯作者：
Dokholyan NV