Pairwise and Multimeric Protein-Protein Docking Using the LZerD Program Suite
Pairwise and Multimeric Protein-Protein Docking Using the LZerD Program Suite
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DOI：
10.1007/978-1-4939-0366-5_15
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发表时间：
2014-01-01
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影响因子：
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通讯作者：
Kihara, Daisuke
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作者：
Esquivel-Rodriguez, Juan;Filos-Gonzalez, Vianney;Kihara, Daisuke
蛋白质之间的物理相互作用涉及许多重要的细胞功能，是理解生物过程机制的关键。蛋白质-蛋白质对接程序提供了一种从蛋白质复合物的组成蛋白质单元计算构建蛋白质复合物结构的三维（3D）模型的方法。蛋白质对接程序需要两个或多个单独的3D蛋白质结构，这是实验解决或计算建模，并输出一系列可能的复杂structure.In本章中，我们提出了LZerD蛋白质对接套件，其中包括成对对接程序，LZerD和PI-LZerD，和多个蛋白质对接，多LZerD，由我们的小组开发的。PI-LZerD将蛋白质对接界面残基作为额外的输入信息。该方法使用基于形状的蛋白质表面特征以及基于物理学的评分项的组合来生成蛋白质复合物模型。这些程序作为独立程序提供，可以从http://kiharalab.org/proteindocking下载。
Physical interactions between proteins are involved in many important cell functions and are key for understanding the mechanisms of biological processes. Protein-protein docking programs provide a means to computationally construct three-dimensional (3D) models of a protein complex structure from its component protein units. A protein docking program takes two or more individual 3D protein structures, which are either experimentally solved or computationally modeled, and outputs a series of probable complex structures.In this chapter we present the LZerD protein docking suite, which includes programs for pairwise docking, LZerD and PI-LZerD, and multiple protein docking, Multi-LZerD, developed by our group. PI-LZerD takes protein docking interface residues as additional input information. The methods use a combination of shape-based protein surface features as well as physics-based scoring terms to generate protein complex models. The programs are provided as stand-alone programs and can be downloaded from http://kiharalab.org/proteindocking.