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CABS-flex 独立版：用于快速建模蛋白质柔性的模拟环境。

CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.

机构信息

Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.

College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.

出版信息

Bioinformatics. 2019 Feb 15;35(4):694-695. doi: 10.1093/bioinformatics/bty685.

DOI:10.1093/bioinformatics/bty685
PMID:30101282
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6379018/
Abstract

SUMMARY

CABS-flex standalone is a Python package for fast simulations of protein structure flexibility. The package combines simulations of protein dynamics using CABS coarse-grained protein model with the reconstruction of selected models to all-atom representation and analysis of modeling results. CABS-flex standalone is designed to allow for command-line access to the CABS computations and complete control over simulation process. CABS-flex standalone is equipped with features such as: modeling of multimeric and large-size protein systems, contact map visualizations, analysis of similarities to the reference structure and configurable modeling protocol. For instance, the user may modify the simulation parameters, distance restraints, structural clustering scheme or all-atom reconstruction parameters. With these features CABS-flex standalone can be easily incorporated into other methodologies of structural biology.

AVAILABILITY AND IMPLEMENTATION

CABS-flex standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. CABS-flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS-flex standalone repository at https://bitbucket.org/lcbio/cabsflex.

摘要

摘要

CABS-flex standalone 是一个用于快速模拟蛋白质结构灵活性的 Python 包。该软件包将使用 CABS 粗粒化蛋白质模型进行蛋白质动力学模拟与选择模型到全原子表示的重建以及建模结果的分析相结合。CABS-flex standalone 旨在允许通过命令行访问 CABS 计算并完全控制模拟过程。CABS-flex standalone 具有以下功能：多聚体和大型蛋白质系统的建模、接触图可视化、与参考结构的相似性分析以及可配置的建模协议。例如，用户可以修改模拟参数、距离约束、结构聚类方案或全原子重建参数。有了这些特性，CABS-flex standalone 可以很容易地集成到结构生物学的其他方法中。

可用性和实现

CABS-flex standalone 遵循 MIT 许可证分发，学术和非营利用户均可免费使用。它是用 Python 实现的。CABS-flex 的源代码、带有使用示例的维基以及适用于 Linux、macOS 和 Windows 的安装说明可从 CABS-flex standalone 的存储库（https://bitbucket.org/lcbio/cabsflex）获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/97e7/6379018/1402bd232426/bty685f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/97e7/6379018/1402bd232426/bty685f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/97e7/6379018/1402bd232426/bty685f1.jpg

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