PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
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DOI：
10.1093/bioinformatics/btq007
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发表时间：
2010-03-01
期刊：
影响因子：
5.8
通讯作者：
Gray, Jeffrey J.
中科院分区：
文献类型：
--
作者：
Chaudhury, Sidhartha;Lyskov, Sergey;Gray, Jeffrey J.
PyRosetta 是 Rosetta 分子建模包的基于 Python 的独立实现，允许用户使用主要的 Rosetta 采样和评分功能编写自定义结构预测和设计算法。 PyRosetta 包含与定义 Rosetta 函数的库的 Python 绑定，包括用于访问和操作蛋白质结构、计算能量和运行基于蒙特卡罗的模拟的函数。 PyRosetta 可以通过两种方式使用：(i) 使用 iPython 以交互方式使用；(ii) 使用 Python 脚本基于脚本。交互模式包含许多帮助功能，非常适合初学者，而脚本模式最适合算法开发。 PyRosetta 具有与 Rosetta 类似的计算性能，可以轻松扩展以用于集群应用，并已用于演示蛋白质对接、蛋白质折叠、循环建模和设计的算法。
PyRosetta is a stand- alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the major Rosetta sampling and scoring functions. PyRosetta contains Python bindings to libraries that define Rosetta functions including those for accessing and manipulating protein structure, calculating energies and running Monte Carlo-based simulations. PyRosetta can be used in two ways: (i) interactively, using iPython and (ii) script-based, using Python scripting. Interactive mode contains a number of help features and is ideal for beginners while script-mode is best suited for algorithm development. PyRosetta has similar computational performance to Rosetta, can be easily scaled up for cluster applications and has been implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design.