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首页> 外文期刊>Acta crystallographica. Section D, Structural biology >Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
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Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0

机译：大规模蛋白质动力学的发展和cryoEM: ProDy 2.0的案例研究

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摘要

Cryo-electron microscopy (cryoEM) has become a well established technique with the potential to produce structures of large and dynamic supramolecular complexes that are not amenable to traditional approaches for studying structure and dynamics. The size and low resolution of such molecular systems often make structural modelling and molecular dynamics simulations challenging and computationally expensive. This, together with the growing wealth of structural data arising from cryoEM and other structural biology methods, has driven a trend in the computational biophysics community towards the development of new pipelines for analysing global dynamics using coarse-grained models and methods. At the centre of this trend has been a return to elastic network models, normal mode analysis (NMA) and ensemble analyses such as principal component analysis, and the growth of hybrid simulation methodologies that make use of them. Here, this field is reviewed with a focus on ProDy, the Python application programming interface for protein dynamics, which has been developed over the last decade. Two key developments in this area are highlighted: (i) ensemble NMA towards extracting and comparing the signature dynamics of homologous structures, aided by the recent SignDy pipeline, and (ii) pseudoatom fitting for more efficient global dynamics analyses of large and low-resolution supramolecular assemblies from cryoEM, revisited in the CryoDy pipeline. It is believed that such a renewal and extension of old models and methods in new pipelines will be critical for driving the field forward into the next cryoEM revolution.
机译：低温电子显微镜(cryoEM)已成为一个良好的技术潜力生产大型结构和动态超分子复合物,并不适合研究结构和的传统方法动力学。分子系统通常使结构造型和分子动力学模拟的挑战和计算昂贵。与日益增长的财富结构数据因cryoEM和其他结构生物学计算方法,推动了这一趋势生物物理学社区的发展新的全球动力学分析使用管道粗粒度的模型和方法。这一趋势已恢复弹性网络模型(NMA)和正常模式分析整体分析,如主成分分析和混合模拟的发展方法利用他们。与关注ProDy场了,Python应用程序编程接口蛋白质动力学,已发展了过去的十年。突出显示区域:(i)合奏NMA方向提取和比较签名动力学同源结构,由于最近SignDy管道,和(2)伪原子适合更高效的大型全球动力学分析和低分辨率的超分子组装cryoEM,重新审视CryoDy管道。相信这样的更新和扩展在新管道将模型和方法驾驶的关键领域向前进接下来cryoEM革命。

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