论文标题
GPU加速枚举和探索HP模型基因型 - 表型图,用于蛋白质折叠
GPU accelerated enumeration and exploration of HP model genotype-phenotype maps for protein folding
论文作者
论文摘要
进化可以用基因型的突变和随后的表型的选择来广泛描述。因此,给定基因型 - 表型(GP)图的全部枚举是检查进化景观的强大技术。但是,由于基因型的数量通常会随基因组长度成倍增长,因此这种计算迅速变得棘手。在这里,我将图形处理单元(GPU)技术应用于疏水极光(HP)模型中的蛋白质折叠模型。该GP图是一个简单且研究的模型,用于蛋白质折叠的复杂过程。对相对较小的2D和3D晶格的先前研究已仅使用常规中央处理单元(CPU)方法进行。通过使用GPU技术,我能够再现Li等人的开拓性计算。[1]在CPU上加快580-700倍的速度。我还能够执行最大的枚举,截至6x6晶格的日期。这些新颖的计算提供了证据,表明流行的“李子布丁”隐喻表明在基因型空间中断开表型并未描述数据。相反,连接的基因型网络的“意大利面”隐喻可能更合适。此外,数据允许探索GP空间内的可设计性与复杂性之间的关系。 GPU方法似乎非常适合TOGP映射,这项工作的成功为其在该领域的更广泛应用提供了有希望的介绍。
Evolution can be broadly described in terms of mutations of the genotype and the subsequent selection of the phenotype. The full enumeration of a given genotype-phenotype (GP) map is therefore a powerful technique in examining evolutionary landscapes. However, because the number of genotypes typically grows exponentially with genome length, such calculations rapidly become intractable. Here I apply graphics processing unit(GPU) techniques to the hydrophobic-polar (HP)model for protein folding. This GP map is a simple and well-studied model for the complex process of protein folding. Prior studies on relatively small 2D and 3D lattices have been exclusively carried out using conventional central processing unit (CPU) approaches. By using GPU techniques, I was able to reproduce the pioneering calculations of Li et al.[1] with a speed up of 580-700 fold over a CPU. I was also able to perform the largest enumeration to date of the 6x6 lattice. These novel calculations provide evidence that a popular "plum-pudding" metaphor that suggests that phenotypes are disconnected in genotype space does not describe the data. Instead a "spaghetti" metaphor of connected genotype networks may be more suitable. Furthermore, the data allows the relationships between designability and complexity within GP space to be explored. GPU approaches appear extremely well suited toGP mapping and the success of this work provides a promising introduction for its wider application in this field.