A heuristic method to bias protein's primary sequence in protein structure prediction

N. Mozayani, Hossein Parineh
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引用次数: 1

Abstract

Protein Structure Prediction (PSP) is one of the most studied topics in the field of bioinformatics. Regarding the intrinsic hardness of the problem, during last decades several computational methods mainly based on artificial intelligence have been proposed to approach the problem. In this paper we broke the main process of PSP into two steps. The first step is making a bias in the sequence, i.e. providing a very fast yet considerably better energy of conformation compared to the primary sequence with zero energy. The second step, which is studied in the other essay, is feeding this biased sequence to another algorithm to find the best possible conformation. For the first step, we developed a new heuristic method to find a low-energy structure of a protein. The main concept of this method is based on rule extraction from previously determined conformations. We'll call this method Fast-Bias-Algorithm (FBA) mainly because it provides a modified structure with better energy from a primary (linear) structure of a protein in a remarkably short time, comparing to the time needed for the whole process. This method was implemented in Netlogo. We have tested this algorithm on several benchmark sequences ranging from 20 to 50-mers in two dimensional Hydrophobic Hydrophilic lattice models. Comparing with the result of the other algorithms, our method in less than 2% of their time reached up to 62% of the energy of their best conformation.
蛋白质结构预测中一阶序列偏差的启发式方法
蛋白质结构预测是生物信息学领域研究最多的课题之一。由于这一问题的内在困难,在过去的几十年中,人们提出了几种主要基于人工智能的计算方法来解决这一问题。在本文中,我们将PSP的主要过程分为两个步骤。第一步是在序列中进行偏置,即与零能量的主序列相比,提供非常快但明显更好的构象能量。第二步是在另一篇文章中研究的,将这个有偏差的序列输入到另一个算法中,以找到可能的最佳构象。第一步,我们开发了一种新的启发式方法来寻找蛋白质的低能量结构。该方法的主要概念是基于从先前确定的构象中提取规则。我们将这种方法称为Fast-Bias-Algorithm (FBA),主要是因为与整个过程所需的时间相比,它可以在非常短的时间内从蛋白质的初级(线性)结构中提供具有更好能量的修饰结构。该方法在Netlogo中实现。我们已经在几个基准序列上测试了该算法,范围从20到50-mers的二维疏水亲水性晶格模型。与其他算法的结果相比,我们的方法在不到2%的时间内达到了最佳构象能量的62%。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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