为什么蛋白质接触网络的小世界不是更小
Why aren't the small worlds of protein contact networks smaller
摘要：
通过计算机实验研究了蛋白质接触网络（由蛋白质氨基酸残基之间的空间接触引起的网络）的平均最短路径长度为何不短，尽管它们对蛋白质折叠很重要。我们发现，较短的平均节点间的距离是不能保证找到一个更容易的全局最优。实验结果也导致了与现有观点相一致的观察结果，即短程或长程相互作用都不主导蛋白质折叠过程。尽管如此，在使用远程交互时稍微延迟的运行产生了最好的搜索性能。我们将这一发现纳入优化功能，给予更多的权重，短程链接。这产生的结果表明，随机化的长距离链接并没有产生更好的搜索性能比蛋白质接触网络自然，即使随机化的长距离链接显着减少平均路径长度，并保留了大部分的集群和正度度相关性固有的蛋白质接触网络。因此，在蛋白质接触网络的拓扑限制之下，除了排除体积的论点之外，还可以有其他解释。
英文摘要：
Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to protein folding. We find that shorter average inter-nodal distances is no guarantee of finding a global optimum more easily. Results from the experiments also led to observations which parallel an existing view that neither short-range nor long-range interactions dominate the protein folding process. Nonetheless, runs where there was a slight delay in the use of long-range interactions yielded the best search performance. We incorporate this finding into the optimization function by giving more weight to short-range links. This produced results showing that randomizing long-range links does not yield better search performance than protein contact networks au natural even though randomizing long-range links significantly reduces average path lengths and retains much of the clustering and positive degree-degree correlation inherent in protein contact networks. Hence there can be explanations, other than the excluded volume argument, beneath the topological limits of protein contact networks.
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