LoopTK: Protein Loop Kinematic Toolkit

Analyzing the motion of flexible protein loops is becoming increasingly important in understanding the various roles that proteins play in human body. LoopTK is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints. LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.LoopTK was developed in close collaboration with the Joint Center for Structural Genomics (JCSG) at the Stanford Linear Accelerator Center. Now a part of the JCSG's protein structure determination process, loopTK models missing protein fragments into experimental data (http://smb.slac.stanford.edu/XpleoServer/Xpleo.jsp).This material is based upon work supported by the National Science Foundation under Grant No. 0443939. Any opinions, findings, and conclusions or recommendations expressed in the above material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=214#pack_288">LoopTK </a> : LoopTK source and documentation </li> </ul>

解析柔性蛋白质环的运动在理解蛋白质在人体中扮演的多种角色方面日益显得至关重要。LoopTK是一款基于C++面向对象的工具包，它模拟蛋白质链的运动学并提供探索其运动空间的方法。在LoopTK中，蛋白质链被建模为一种机器人操作器，其中键作为臂，二面角自由度作为关节。LoopTK专门设计用于模拟蛋白质环的运动学，但也可用于分析蛋白质链任何部分的运动。LoopTK提供了采样蛋白质环构象空间以及环的自运动空间的方法。LoopTK的示例应用包括X射线晶体学、同源建模和药物设计。LoopTK是在与斯坦福线性加速器中心联合结构基因组学中心（JCSG）的紧密合作下开发的。如今，LoopTK已成为JCSG蛋白质结构解析流程的一部分，将缺失的蛋白质片段模拟为实验数据（http://smb.slac.stanford.edu/XpleoServer/Xpleo.jsp）。本材料基于美国国家科学基金会资助的研究成果（项目编号：0443939）。上述材料中表达的观点、发现、结论或建议均为作者观点，并不必然反映美国国家科学基金会的立场。

本项目包含以下软件/数据包：

<ul>
<li><a href="https://simtk.org/frs?group_id=214#pack_288">LoopTK</a> : LoopTK源代码和文档</li>
</ul>