Volume 46, Issue 1 e27516
RESEARCH ARTICLE

Assessing small molecule conformational sampling methods in molecular docking

Qiancheng Xia

Qiancheng Xia

Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China

National Institute of Biological Sciences, Beijing, China

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Qiuyu Fu

Qiuyu Fu

National Institute of Biological Sciences, Beijing, China

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Cheng Shen

Cheng Shen

National Institute of Biological Sciences, Beijing, China

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Ruth Brenk

Ruth Brenk

Department of Biomedicine, University of Bergen, Bergen, Norway

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Niu Huang

Corresponding Author

Niu Huang

Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China

National Institute of Biological Sciences, Beijing, China

Correspondence

Niu Huang, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China.

Email: [email protected]

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First published: 30 October 2024
Citations: 1

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.

DATA AVAILABILITY STATEMENT

The code for db2_converter, the DB2 files, and the prepared protein structures are available upon request.

The full text of this article hosted at iucr.org is unavailable due to technical difficulties.