蛋白质体系中与氨基酸相关的主链挠能项
Amino-acid-dependent main-chain torsion-energy terms for protein systems
摘要：
许多常用的蛋白质体系力场，如AMBER、CHARMM、GROMACS、OPLS和ECEPP，都具有与氨基酸无关的主链扭转能项力场参数。在这里，我们提出了一种新的类型的氨基酸依赖的扭转能量项的力场。作为一个例子，我们将这种方法应用于AMBER ff 03力场，并通过使用我们的优化方法，这是一种基于知识的方法，确定了新的氨基酸依赖的参数$ψ$和$ψ'$角为每个氨基酸。为了测试新的力场参数的有效性，我们然后进行折叠模拟$α$ -螺旋和$β$ -发夹肽，使用优化的力场。结果表明，新的力场参数给出的结构比原来的AMBER ff 03力场更符合实验的含义。
英文摘要：
Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for $ψ$ and $ψ'$ angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of $α$-helical and $β$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field.
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