Vendruscolo M, Domany E
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
Vitam Horm. 2000;58:171-212. doi: 10.1016/s0083-6729(00)58025-x.
We discuss the problem of representations of protein structure and give the definition of contact maps. We present a method to obtain a three-dimensional polypeptide conformation from a contact map. We also explain how to deal with the case of nonphysical contact maps. We describe a stochastic method to perform dynamics in contact map space. We explain how the motion is restricted to physical regions of the space. First, we introduce the exact free energy of a contact map and discuss two simple approximations to it. Second, we present a method to derive energy parameters based on perception learning. We prove in an extensive number of situations that the pairwise contact approximation both when alone and when supplemented with a hydrophobic term is unsuitable for stabilizing proteins' native states.
我们讨论了蛋白质结构表示的问题，并给出了接触图的定义。我们提出了一种从接触图获得三维多肽构象的方法。我们还解释了如何处理非物理接触图的情况。我们描述了一种在接触图空间中执行动力学的随机方法。我们解释了运动是如何被限制在空间的物理区域的。首先，我们引入了接触图的精确自由能，并讨论了对其的两种简单近似。其次，我们提出了一种基于感知学习推导能量参数的方法。我们在大量情况下证明，单独的成对接触近似以及补充疏水项时，都不适用于稳定蛋白质的天然状态。
