基于 PLUMED-ISDB 的综合结构与动态生物学。
Integrative structural and dynamical biology with PLUMED-ISDB.
机构信息
Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
Department of Chemistry, Institute for Advanced Study, Technische Universität München, Garching 85747, Germany.
出版信息
Bioinformatics. 2017 Dec 15;33(24):3999-4000. doi: 10.1093/bioinformatics/btx529.
SUMMARY
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.
AVAILABILITY AND IMPLEMENTATION
PLUMED-ISDB is freely available at www.plumed.org.
CONTACT
mb2006@cam.ac.uk or carlo.camilloni@unimi.it.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
通过将实验数据与先验物理化学知识进行适当组合，可以获得生物系统的准确结构模型。本文介绍了 PLUMED-ISDB，这是流行的 PLUMED 库的一个开源、免费的模块，通过将实验数据与先验信息相结合，实现构象异质系统的结构和动力学的同时确定。这种集成是使用元推断来实现的，元推断是一个通用的贝叶斯框架，考虑了数据中的噪声及其集合平均性质。PLUMED-ISDB 实现了多种类型的实验数据，例如几种 NMR 观测值、FRET、SAXS 和冷冻电子显微镜数据，并使用各种增强采样方法和系统分辨率，实现了单个蛋白质、蛋白质复合物、膜蛋白、RNA 和 DNA 的结构和动力学建模。
可用性和实现
PLUMED-ISDB 可在 www.plumed.org 上免费获得。
联系方式
mb2006@cam.ac.uk 或 carlo.camilloni@unimi.it。
补充信息
补充数据可在“Bioinformatics”在线获取。
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