Irbäck Anders, Troein Carl
J Biol Phys. 2002 Mar;28(1):1-15. doi: 10.1023/A:1016225010659.
The hydrophobic/polar HP model on the square lattice has been widely used toinvestigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the number of contacts, the upper limit on the chain length N has been 18-20 because of the rapid exponential growth of thenumbers of conformations and sequences. We show how a few optimizations push this limit by about 5 units. Based on these calculations, we study the statistical distribution of hydrophobicity along designing sequences. We find that the average number of hydrophobic and polar clumps along the chains is larger for designing sequences than for random ones, which is in agreement with earlier findings for N ≤ 18 and with results for real enzymes. We also show that this deviation from randomness disappears if the calculations are restricted to maximally compact structures.
方格晶格上的疏水/极性（HP）模型已被广泛用于研究蛋白质折叠的基础。在所有设计序列（具有唯一基态的序列）被无接触数量限制地枚举的情况下，由于构象和序列数量的快速指数增长，链长N的上限一直是18 - 20。我们展示了一些优化如何将这个极限提高约5个单位。基于这些计算，我们研究了沿设计序列的疏水性统计分布。我们发现，与随机序列相比，设计序列沿链的疏水和极性团块的平均数量更多，这与N≤18时的早期发现以及真实酶的结果一致。我们还表明，如果计算仅限于最大紧凑结构，这种与随机性的偏差就会消失。
