Integrative structural and dynamical biology with PLUMED-ISDB
Integrative structural and dynamical biology with PLUMED-ISDB
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DOI：
10.1093/bioinformatics/btx529
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发表时间：
2017-12-15
期刊：
影响因子：
5.8
通讯作者：
Camilloni, Carlo
中科院分区：
文献类型：
--
作者：
Bonomi, Massimiliano;Camilloni, Carlo
生物系统的精确结构模型可以通过将实验数据与先验物理化学知识适当地结合来获得。在这里，我们提出了PLUMED-ISDB，一个开源的，免费提供的模块流行的PLUMED库，它使同时确定的构象异构系统的结构和动力学通过整合实验数据与先验信息。这种整合是使用metainference来实现的，metainference是一种通用的贝叶斯框架，它既考虑了数据中的噪声，也考虑了它们的整体平均性质。PLUMED-ISDB实现了不同类型的实验数据，如几个NMR观测值，FRET，SAXS和低温电子显微镜数据，并能够使用各种增强的采样方法和系统分辨率对单个蛋白质，蛋白质复合物，膜蛋白，RNA和DNA的结构和动力学进行建模。
Accurate structural models of biological systems can be obtained by properly combining experimental data with a priori physico-chemical knowledge. Here we present PLUMED-ISDB, an open-source, freely-available module of the popular PLUMED library, which enables the simultaneous determination of structure and dynamics of conformationally heterogeneous systems by integrating experimental data with a priori information. This integration is achieved using metainference, a general Bayesian framework that accounts for both noise in the data and their ensemble-averaged nature. PLUMED-ISDB implements different types of experimental data, such as several NMR observables, FRET, SAXS and cryo-electron microscopy data, and enables modelling structure and dynamics of individual proteins, protein complexes, membrane proteins, RNA and DNA, using a variety of enhanced sampling methods and resolutions of the system.