每一个在特定姿态的RMSD(通常为1.5-2˚Å)42范围内预测姿态的附加对接程序,都会增加该姿态的共识水平,而更高的共识水平意味着更可靠的姿态。这一知识有助于过滤非结合配体。9、42 Ren等人在一项相关研究中,与多个对接程序进行了对接,计算了每个程序预测的顶部姿态与其他程序预测的顶部姿态的RMSD总和。总RMSD定义...
然后执行rms模块,选择"Backbone"来进行最小二乘法拟合,选择"JZ4_Heavy"计算RMSD。这样可以通过拟合来消除蛋白质的转动和平动,得到的RMSD对应着JZ4的位置相对于蛋白质变化了多少,这可以很好地说明在模拟过程中配体的结合姿态维持的好不好。 gmx rms -s em.tpr -f md_0_10_center.xtc -n index.ndx -tu ns ...
experimentally observed binding pose of the ligand in the binding pocket is excellently reproduced with a root mean square deviation (RMSD) of 1.4 ± 0.2 Å, which is similar to the one from atomistic studies37. Fig.1cvisualizes the benzene density around L99A T4 lysozyme. The ...
Similar to PDBbind, positive and negative samples are determined with RMSD. Protease data were largely directed into the training set while the other targets, with the exception of on non-structural protein, were directed to the test set. This variety allows the inclusion of the critical targets...
EDM-Dock在RMSD和成功率方面都表现出优异的表现。此外,我们的方法不需要耗时的搜索算法来枚举许多可能的停靠姿势或侧链构象,从而显著增加了速度和效率。综上所述,这些因素表明深度学习模型能够灵活有效地对接蛋白质-配体。这种方法是一种强大的新范式,将被进一步研究并用于加速现代基于结构的药物发现。
We demonstrate that allowing these side chains to assume rotameric conformations enables the successful cross docking of 19 complexes (ligand all atom RMSD<2.0) using our docking software FLIPDock. The number of side receptor side chains interacting with a ligand can vary according to the ligand'...
For targets with approximately correct global topology (RMSD <8 Å), all three methods have a reasonable ability to predict the ligand binding pocket. Nevertheless, COFACTOR generates 15% and 92% more correct (distance error <4.5 Å) binding pocket predictions than FINDSITE and ConCavity (...
LigDockCSA finds the best scoring poses within 2 Å root-mean-square deviation (RMSD) from the native structures for 84.7% of the test cases, compared to 81.7% for AutoDock and 80.5% for GOLD. The results improve further to 89.4% by incorporating the conformational entropy. 2011 ...
For rigid ligands, H-DOCK was tested on a set of 271 complexes where there is at least one intermolecular hydrogen bond, and H-DOCK achieved success rate (RMSD<2.0鈥壝 ) of 91.1%. For flexible ligands, H-DOCK was tested on another set of 93 complexes, where each case was a ...
数据集包括 PDBbind v2020 的通用集作为训练集,CASF-2016 作为测试集,为了公平比较,删除了数据重叠。 BindNet在预训练阶段已经学习了结构复杂的信息,因此,我们用去除重叠的数据重新训练它。我们的评估指标涉及计算预测位置和实际位置之间的均方根偏差 (RMSD),显示低于阈值的值的百分比。