GalaxyDock2-HEME：血红素蛋白的蛋白质-配体对接,Journal of Computational Chemistry

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GalaxyDock2-HEME：血红素蛋白的蛋白质-配体对接
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2023-02-21 , DOI: 10.1002/jcc.27092
Changsoo Lee ₁ , Jinsol Yang ₂ , Sohee Kwon ₂ , Chaok Seok _{1,

2}

Affiliation

蛋白质-配体结合姿势的预测是理解蛋白质-配体相互作用和计算机辅助药物设计的重要组成部分。各种蛋白质都涉及辅基，例如血红素的功能，充分考虑辅基对于蛋白质-配体对接至关重要。在这里，我们扩展了 GalaxyDock2 蛋白-配体对接算法来处理与血红素蛋白的配体对接。与血红素蛋白的对接涉及增加的复杂性，因为血红素铁和配体的相互作用具有共价性质。GalaxyDock2-HEME 是一种新的血红素蛋白-配体对接程序，它是在 GalaxyDock2 的基础上通过添加方向依赖性评分项来描述血红素铁-配体配位相互作用而开发的。这个新的对接程序比其他非商业对接程序（例如 EADock with MMBP、AutoDock Vina、PLANTS、LeDock 和 GalaxyDock2）在已知配体与铁结合的血红素蛋白-配体对接基准组上表现更好。此外，对配体不与铁结合的另外两组血红素蛋白-配体复合物的对接结果表明，与其他对接程序相比，GalaxyDock2-HEME 对铁结合的偏倚不高。这意味着新的对接程序可以区分血红素蛋白的铁结合剂和非铁结合剂。另外两组血红素蛋白-配体复合物的对接结果表明，与其他对接程序相比，GalaxyDock2-HEME 对铁结合的偏倚不高。这意味着新的对接程序可以区分血红素蛋白的铁结合剂和非铁结合剂。另外两组血红素蛋白-配体复合物的对接结果表明，与其他对接程序相比，GalaxyDock2-HEME 对铁结合的偏倚不高。这意味着新的对接程序可以区分血红素蛋白的铁结合剂和非铁结合剂。

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GalaxyDock2-HEME: Protein–ligand docking for heme proteins

Prediction of protein–ligand binding poses is an essential component for understanding protein–ligand interactions and computer-aided drug design. Various proteins involve prosthetic groups such as heme for their functions, and adequate consideration of the prosthetic groups is vital for protein–ligand docking. Here, we extend the GalaxyDock2 protein–ligand docking algorithm to handle ligand docking to heme proteins. Docking to heme proteins involves increased complexity because the interaction of heme iron and ligand has covalent nature. GalaxyDock2-HEME, a new protein–ligand docking program for heme proteins, has been developed based on GalaxyDock2 by adding an orientation-dependent scoring term to describe heme iron-ligand coordination interaction. This new docking program performs better than other noncommercial docking programs such as EADock with MMBP, AutoDock Vina, PLANTS, LeDock, and GalaxyDock2 on a heme protein–ligand docking benchmark set in which ligands are known to bind iron. In addition, docking results on two other sets of heme protein–ligand complexes in which ligands do not bind iron show that GalaxyDock2-HEME does not have a high bias toward iron binding compared to other docking programs. This implies that the new docking program can distinguish iron binders from noniron binders for heme proteins.

更新日期：2023-02-21

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