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Perspective on computational simulations of glycosaminoglycans.
Wiley Interdisciplinary Reviews: Computational Molecular Science ( IF 16.8 ) Pub Date : 2018-09-10 , DOI: 10.1002/wcms.1388
Balaji Nagarajan 1, 2 , Nehru Viji Sankaranarayanan 1, 2 , Umesh R Desai 1, 2
Affiliation  

Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.

中文翻译:

糖胺聚糖的计算模拟的观点。

糖胺聚糖 (GAG) 因其巨大的结构复杂性而成为化学家、生物化学家、生物学家、药物化学家和药物输送专家的一个艰巨的前沿领域。GAG 可以说是最复杂的天然线性生物聚合物,其理论上的多样性比蛋白质和核酸高出几个数量级。然而,这种多样性总体上尚未得到开发。计算方法提供了了解 GAG 结构和动力学的主要途径,从而实现这些生物聚合物的新应用。事实上,计算算法、软件、在线工具和技术已经达到了一定的复杂程度,有助于理解构象变异的原子细节和单个 GAG 序列的蛋白质识别。这篇综述描述了 GAG 计算研究的当前方法和挑战。它介绍了自最早提及 GAG(20 世纪 60 年代)以来的主要发现历史、GAG 特有的参数和力场的开发,以及这些工具在理解 GAG 结构-功能关系方面的应用。这篇综述还介绍了如何进行 GAG 模拟的部分,该部分针对有兴趣进入这个有潜力影响治疗的前景广阔的领域的研究人员。
更新日期:2018-09-10
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