CaFE: a tool for binding affinity prediction using end-point free energy methods
CaFE: a tool for binding affinity prediction using end-point free energy methods
复制标题
CaFE：使用终点自由能方法进行结合亲和力预测的工具
DOI：
10.1093/bioinformatics/btw215
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发表时间：
2016-07-15
期刊：
影响因子：
5.8
通讯作者：
Hou, Tingjun
中科院分区：
文献类型：
--
作者：
Liu, Hui;Hou, Tingjun
结合自由能的准确预测对于计算生物学和基于结构的药物设计特别重要。在这些结合亲和力预测的方法中，终点方法，如MM/PBSA和LIE，已被广泛使用，因为它们可以在预测精度和计算成本之间取得良好的平衡。在这里，我们提出了一个名为自由能计算 (CaFE) 的易于使用的管道工具，用于进行 MM/PBSA 和 LIE 计算。在 VMD 和 NAMD 程序的支持下，CaFE 能够处理由不同分子模拟软件包生成的多种静态坐标和分子动力学轨迹文件格式，并支持各种力场参数。可用性和实施：CaFE 源代码和文档可在 GNU 通用公共许可证下通过 GitHub 免费获取：https://github.com/huiliucode/cafe_plugin。它是一个用 Tcl 编写的 VMD 插件，使用与平台无关。
Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. Availability and implementation: CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin. It is a VMD plugin written in Tcl and the usage is platform-independent.