Protein docking algorithms aim to predict the 3D structure of a protein complex from the structures of its separated components. In the past, most docking algorithms focused on docking pairs of proteins to form dimeric complexes. However, attention is now turning towards the more difficult problem of using docking methods to predict the structures of multicomponent complexes. In both cases, however, the constituent proteins often change conformation upon complex formation, and this can cause many algorithms to fail to detect near‐native binding orientations due to the high number of atomic steric clashes in the list of candidate solutions. An increasingly popular way to retain more near‐native orientations is to define one or more restraints that serve to modulate or override the effect of steric clashes. Here, we present an updated version of our “EROS‐DOCK” docking algorithm which has been extended to dock arbitrary dimeric and trimeric complexes, and to allow the user to define residue‐residue or atom‐atom interaction restraints. Our results show that using even just one residue‐residue restraint in each interaction interface is sufficient to increase the number of cases with acceptable solutions within the top 10 from 51 to 121 out of 173 pairwise docking cases, and to successfully dock 8 out of 11 trimeric complexes.

中文翻译：

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在EROS-DOCK中使用约束可提高配对和多组分蛋白质对接中的模型质量。

蛋白质对接算法旨在根据其分离成分的结构预测蛋白质复合物的3D结构。过去，大多数对接算法都专注于对蛋白质对接以形成二聚体复合物。但是，现在的注意力转向使用对接方法预测多组分复合物结构的更困难的问题。但是，在这两种情况下，组成蛋白通常会在复杂的形成过程中改变构象，由于候选溶液列表中原子空间冲突的数量众多，这可能导致许多算法无法检测到接近天然的结合方向。保持更接近本机方向的一种越来越流行的方法是定义一个或多个约束，这些约束用于调节或覆盖空间冲突的影响。这里，我们提出了“ EROS-DOCK”对接算法的更新版本，该算法已扩展为可对接任何二聚体和三聚体复合物，并允许用户定义残基-残基或原子-原子相互作用约束。我们的结果表明，在每个交互界面中甚至只使用一个残基-残基约束条件，就足以将前10名中可接受解决方案的案例数从173个成对对接案例中的51个增加到121个，并成功对接11个案例中的8个三聚体。