Lasters I, Desmet J
Corvas International, N.V., Gent, Belgium.
Protein Eng. 1993 Sep;6(7):717-22. doi: 10.1093/protein/6.7.717.
Recently it has been shown that the dead-end elimination theorem is a powerful tool in the search for the global minimum energy conformation (GMEC) of a large collection of protein side chains given known backbone coordinates and a library of allowed side chain conformational states, also known as rotamers. A side chain placement algorithm based on this theorem iteratively applies this theorem to single as well as to pairs of rotamers leading to the identification of rotamers, single or pairs, that are incompatible with the GMEC and that can thus be qualified as 'dead-ending'. Here we formulate a theorem which proves that contrary to intuition dead-end rotamer pairs cannot simply be discarded from consideration in the iterative process leading to the further elimination of dead-end rotamers. We refer to this theorem as the fuzzy-end elimination theorem. We also describe how the obtained dead-end rotamer pairs can contribute to the search for the GMEC in the protein side chain placement problem. Hence the present work forms a theoretical basis for the correct implementation of a side chain placement algorithm based on the dead-end elimination theorem. In addition, possible future perspectives are presented.
最近的研究表明，在已知主链坐标和允许的侧链构象状态库（也称为旋转异构体）的情况下，死端消除定理是寻找大量蛋白质侧链全局最小能量构象（GMEC）的有力工具。基于该定理的侧链放置算法将此定理反复应用于单个旋转异构体以及旋转异构体对，从而识别出与GMEC不兼容、因此可被认定为“死端”的单个或成对旋转异构体。在此，我们提出一个定理，该定理证明，与直觉相反，在导致进一步消除死端旋转异构体的迭代过程中，不能简单地将死端旋转异构体对排除在考虑范围之外。我们将这个定理称为模糊端消除定理。我们还描述了所获得的死端旋转异构体对如何有助于解决蛋白质侧链放置问题中的GMEC搜索。因此，本研究为基于死端消除定理的侧链放置算法的正确实施奠定了理论基础。此外，还提出了可能的未来研究方向。
