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HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

机译：HopDock：蛋白质对接中诱饵采样的概率搜索算法

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Background Elucidating the three-dimensional structure of a higher-order molecular assembly formed by interacting molecular units, a problem commonly known as docking, is central to unraveling the molecular basis of cellular activities. Though protein assemblies are ubiquitous in the cell, it is currently challenging to predict the native structure of a protein assembly in silico. Methods This work proposes HopDock, a novel search algorithm for protein-protein docking. HopDock efficiently obtains an ensemble of low-energy dimeric configurations, also known as decoys, that can be effectively used by ab-initio docking protocols. HopDock is based on the Basin Hopping (BH) framework which perturbs the structure of a dimeric configuration and then follows it up with an energy minimization to explicitly sample a local minimum of a chosen energy function. This process is repeated in order to sample consecutive energy minima in a trajectory-like fashion. HopDock employs both geometry and evolutionary conservation analysis to narrow down the interaction search space of interest for the purpose of efficiently obtaining a diverse decoy ensemble. Results and conclusions A detailed analysis and a comparative study on seventeen different dimers shows HopDock obtains a broad view of the energy surface near the native dimeric structure and samples many near-native configurations. The results show that HopDock has high sampling capability and can be employed to effectively obtain a large and diverse ensemble of decoy configurations that can then be further refined in greater structural detail in ab-initio docking protocols.
机译：背景技术阐明由相互作用的分子单元形成的高阶分子组装体的三维结构，通常被称为对接的问题，是弄清细胞活性的分子基础的关键。尽管蛋白质装配体在细胞中无处不在，但目前预测计算机中蛋白质装配体的天然结构仍具有挑战性。方法这项工作提出了HopDock，一种新颖的蛋白质-蛋白质对接搜索算法。 HopDock有效地获得了低能量二聚体配置（也称为诱饵）的集合，可以从头开始对接协议有效地使用它们。 HopDock基于盆地跳跃（BH）框架，该框架会扰乱二聚体结构的结构，然后对其进行能量最小化以显式采样所选能量函数的局部最小值。重复该过程，以便以类似轨迹的方式采样连续的能量最小值。 HopDock同时使用几何和进化守恒分析来缩小感兴趣的交互搜索空间，以有效地获得多样化的诱饵集合。结果与结论对17种不同的二聚体进行了详细的分析和比较研究，结果表明HopDock可以在天然二聚体结构附近获得广泛的能量表面，并可以对许多近天然构型进行采样。结果表明，HopDock具有很高的采样能力，可用于有效地获得诱饵配置的各种组合，然后可以在从头对接协议中更详细地细化。

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