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首页> 外文期刊>Journal of Molecular Biology >RosettaLigand docking with full ligand and receptor flexibility.
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RosettaLigand docking with full ligand and receptor flexibility.

机译：RosettaLigand对接具有完整的配体和受体柔性。

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Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and ligand-bound states, the conformational flexibility of the protein is typically ignored in protein-small molecule docking programs. We previously described the program RosettaLigand, which leverages the Rosetta energy function and side-chain repacking algorithm to account for flexibility of all side chains in the binding site. Here we present extensions to RosettaLigand that incorporate full ligand flexibility as well as receptor backbone flexibility. Including receptor backbone flexibility is found to produce more correct docked complexes and to lower the average RMSD of the best-scoring docked poses relative to the rigid-backbone results. On a challenging set of retrospective and prospective cross-docking tests, we find that the top-scoring ligand pose is correctly positioned within 2 A RMSD for 64% (54/85) of cases overall.
机译：小分子配体的计算对接成为蛋白质受体是现代药物发现的重要工具。尽管经常在游离态和配体结合态之间观察到构象调整，但是在蛋白质小分子对接程序中通常忽略蛋白质的构象柔性。先前我们描述了RosettaLigand程序，该程序利用Rosetta能量函数和侧链重新打包算法来考虑绑定位点中所有侧链的灵活性。在这里，我们介绍了对RosettaLigand的扩展，其中包括完整的配体柔性以及受体骨架柔性。已发现，包括受体骨架柔性在内，可以产生更正确的对接复合物，并且相对于刚性骨干结果，可以降低得分最高的对接姿势的平均RMSD。在一组具有挑战性的回顾性和前瞻性交叉对接测试中，我们发现得分最高的配体位姿正确定位在2 A RMSD内，占总体病例的64％（54/85）。

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