Assessing small molecule conformational sampling methods in molecular docking
Qiancheng Xia1,2, Qiuyu Fu2, Cheng Shen2
1Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
Abstract:
Small molecule conformational sampling plays a pivotal role in molecular docking. Recent advancements have led to the emergence of various conformational sampling methods, each employing distinct algorithms. This study investigates the impact of different small molecule conformational sampling methods in molecular docking using UCSF DOCK 3.7. Specifically, six traditional sampling methods (Omega, BCL::Conf, CCDC Conformer Generator, ConfGenX, Conformator, RDKit ETKDGv3) and a deep learning-based model (Torsional Diffusion) for generating conformational ensembles are evaluated. These ensembles are subsequently docked against the Platinum Diverse Dataset, the PoseBusters dataset and the DUDE-Z dataset to assess binding pose reproducibility and screening power. Notably, different sampling methods exhibit varying performance due to their unique preferences, such as dihedral angle sampling ranges on rotatable bonds. Combining complementary methods may lead to further improvements in docking performance.
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