Nano-kinematics for analysis of protein molecules
Nano-kinematics for analysis of protein molecules
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DOI：
10.1115/1.1867956
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发表时间：
2005-07-01
影响因子：
3.3
通讯作者：
Alvarado, C
中科院分区：
文献类型：
--
作者：
Kazerounian, K;Latif, K;Alvarado, C
蛋白质是进化的选择机制。纳米机械系统的研究必须包括对蛋白质分子的几何和构象的理解。蛋白质是由旋转关节连接的微型刚体的开环或闭合运动链。运动学社区在扩大纳米生物力学系统的知识边界方面处于独特的地位。在这项工作中，我们提出了一种全面的蛋白质分子运动学符号和直接运动学方法。这些方法利用了零位置分析方法，并借鉴了机器人操作理论中的其他最新进展。作为二面体和旋转角的函数，寻找蛋白质链中每个原子的坐标所涉及的程序在计算上是迄今为止发展起来的最有效的公式。本文件的注释和方法已编入计算机软件包PROTOFOLD，并将提供给有兴趣使用它的个人。PROTOFOLD是一个软件包，它实现了新的和全面的方法来从头开始预测蛋白质的最终三维构象，只给出了它的线性结构。除了上面提到的新的运动学方法，我们还包括了任何涉及蛋白质的运动学分析所需的所有基本运动学参数值。虽然这些值是基于蛋白质数据库中记录的大量知识，但它们是以有利于运动学的形式呈现的。
Proteins are evolution's mechanisms of choice. The study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. In this work, we have presented a comprehensive methodology for kinematics notation and direct kinematics for protein molecules. These methods utilize the zero-position analysis method and draws upon other recent advances in robot manipulation theories. The procedures involved in finding the coordinates of every atom in the protein chain as a function of the dihedral and Rotamer angles are computationally the most efficient formulation developed to date. The notation and the methodologies of this paper are incorporated in the computer software package PROTOFOLD and will be made available to individuals interested in using it. PROTOFOLD is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In addition to the new kinematics methodologies mentioned above, we have also included all the basic kinematic parameter values that are needed in any kinematic analysis involving proteins. While these values are based on a body of knowledge recorded in the protein data bank, they are presented in a form conducive to kinematics.