San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA.
J Comput Chem. 2013 Jul 30;34(20):1743-58. doi: 10.1002/jcc.23304. Epub 2013 May 21.
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.
计算对接是预测大分子复合物的有用工具，而这些复合物通常很难通过实验来确定。在这里，我们介绍 DOT2 软件套件，这是 DOT 分子间对接程序的更新版本。DOT2 提供了基于分子坐标的简单、自动化的改进生物物理模型构建，提供了检查点来指导用户包含关键特征。DOT 已经被更新，以更快地运行，允许在网格大小和间距上具有灵活性，并生成无限数量的有利候选构象的完整列表。输出可以通过实验数据进行过滤，并通过静电和原子去溶剂化能的总和进行重新评分。我们表明，这种重新评分方法可以提高广泛的大分子相互作用的正确复合物的排名，并证明生物相关模型对于生物相关结果是必不可少的。DOT2 的灵活性和多功能性适应了复杂生物系统的现实模型，提高了对接结果成功的可能性。
