Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
PLoS One. 2011;6(8):e23294. doi: 10.1371/journal.pone.0023294. Epub 2011 Aug 24.
The Rosetta de novo structure prediction and loop modeling protocols begin with coarse grained Monte Carlo searches in which the moves are based on short fragments extracted from a database of known structures. Here we describe a new object oriented program for picking fragments that greatly extends the functionality of the previous program (nnmake) and opens the door for new approaches to structure modeling. We provide a detailed description of the code design and architecture, highlighting its modularity, and new features such as extensibility, total control over the fragment picking workflow and scoring system customization. We demonstrate that the program provides at least as good building blocks for ab-initio structure prediction as the previous program, and provide examples of the wide range of applications that are now accessible.
罗塞塔从头结构预测和循环建模协议从粗粒度的蒙特卡罗搜索开始，其中的移动基于从已知结构数据库中提取的短片段。在这里，我们描述了一个用于选择片段的新的面向对象的程序，该程序大大扩展了以前程序（nnmake）的功能，并为结构建模开辟了新的途径。我们提供了代码设计和架构的详细描述，突出了其模块化以及可扩展性、对片段选择工作流程和评分系统定制的完全控制等新功能。我们证明，该程序为从头预测结构提供的构建块至少与以前的程序一样好，并提供了现在可访问的广泛应用的示例。
