Assessing small molecule conformational sampling methods in molecular docking
Qiancheng Xia
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
National Institute of Biological Sciences, Beijing, China
Search for more papers by this authorQiuyu Fu
National Institute of Biological Sciences, Beijing, China
Search for more papers by this authorCheng Shen
National Institute of Biological Sciences, Beijing, China
Search for more papers by this authorRuth Brenk
Department of Biomedicine, University of Bergen, Bergen, Norway
Search for more papers by this authorCorresponding 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]
Search for more papers by this authorQiancheng Xia
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
National Institute of Biological Sciences, Beijing, China
Search for more papers by this authorQiuyu Fu
National Institute of Biological Sciences, Beijing, China
Search for more papers by this authorCheng Shen
National Institute of Biological Sciences, Beijing, China
Search for more papers by this authorRuth Brenk
Department of Biomedicine, University of Bergen, Bergen, Norway
Search for more papers by this authorCorresponding 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]
Search for more papers by this authorAbstract
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.
Open Research
DATA AVAILABILITY STATEMENT
The code for db2_converter, the DB2 files, and the prepared protein structures are available upon request.
Supporting Information
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jcc27516-sup-0001-Supinfo.pdfPDF document, 33.7 MB | Data S1. Supplementary Information. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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