IAVI, Scripps Research Institute, La Jolla, San Diego, California, USA.
J Comput Chem. 2012 Jul 30;33(20):1645-61. doi: 10.1002/jcc.22968. Epub 2012 May 8.
We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open-source software, freely downloadable at http://msl-libraries.org. We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods.
我们介绍了 Molecular Software Library（MSL），这是一个用于分子建模的 C++库。MSL 是一组工具，支持设计、建模和分析大分子的各种算法。该库支持的主要功能包括应用几何变换和对齐的方法、实现丰富的能量函数集、侧链优化、骨架操作、溶剂可及表面积计算以及其他工具。MSL 具有许多独特的功能，例如存储替代原子坐标（用于建模）和同一骨架位置的多个氨基酸身份（用于设计）的能力。它具有扩展其能量函数的简单机制，并且可以与任何类型的分子一起使用。尽管代码库很大，但 MSL 的创建初衷是易于开发。它允许快速实现简单任务，同时完全支持复杂应用程序的创建。这里通过示例展示了该软件的一些潜力，这些示例展示了如何用几行代码来编程复杂而基本的建模任务。MSL 是一个正在进行和不断发展的项目，定期引入新的功能和改进，但它已经成熟，适合生产，并已在许多蛋白质建模和设计项目中使用。MSL 是开源软件，可在 http://msl-libraries.org 免费下载。我们提议将其作为开发新分子算法的通用平台，以促进计算方法的分发、共享和再利用。
