Potential energy functions for protein design
Potential energy functions for protein design
复制标题
蛋白质设计的势能函数
DOI：
10.1016/j.sbi.2007.03.006
复制
发表时间：
2007-04-01
影响因子：
6.8
通讯作者：
Harbury, Pehr B.
中科院分区：
文献类型：
--
作者：
Boas, F. Edward;Harbury, Pehr B.
不同的势能函数在蛋白质动力学模拟、蛋白质设计计算和蛋白质结构预测中占主导地位。显然，同样的物理原理适用于这三种情况。势能函数的不同反映了计算方法的不同。随着计算机能力和算法的提高，同样的势能函数应该适用于这三个问题。在这篇综述中，我们研究了目前用于蛋白质设计的能量函数，并展望了分子力学领域的进展，这些进展可以用于下一代设计算法。我们特别关注了疏水效应、极化和氢键的改进模型。
Different potential energy functions have predominated in protein dynamics simulations, protein design calculations, and protein structure prediction. Clearly, the same physics applies in all three cases. The differences in potential energy functions reflect differences in how the calculations are performed. With improvements in computer power and algorithms, the same potential energy function should be applicable to all three problems. In this review, we examine energy functions currently used for protein design, and look to the molecular mechanics field for advances that could be used in the next generation of design algorithms. In particular, we focus on improved models of the hydrophobic effect, polarization and hydrogen bonding.