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In this study, based on a cross-docking dataset dedicatedly constructed from the PDBbind database, we developed several XGBoost-trained classifiers to discriminate the near-native binding poses from decoys, and systematically assessed their performance with\/without the involvement of the cross-docked poses in the training\/test sets. The calculation results illustrate that using Extended Connectivity Interaction Features (ECIF), Vina energy terms and docking pose ranks as the features can achieve the best performance, according to the validation through the random splitting or refined-core splitting and the testing on the re-docked or cross-docked poses. Besides, it is found that, despite the significant decrease of the performance for the threefold clustered cross-validation, the inclusion of the Vina energy terms can effectively ensure the lower limit of the performance of the models and thus improve their generalization capability. Furthermore, our calculation results also highlight the importance of the incorporation of the cross-docked poses into the training of the SFs with wide application domain and high robustness for binding pose prediction. The source code and the newly-developed cross-docking datasets can be freely available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/sc8668\/ml_pose_prediction\">https:\/\/github.com\/sc8668\/ml_pose_prediction<\/jats:ext-link>and<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/zenodo.org\/record\/5525936\">https:\/\/zenodo.org\/record\/5525936<\/jats:ext-link>, respectively, under an open-source license. We believe that our study may provide valuable guidance for the development and assessment of new machine learning-based SFs (MLSFs) for the predictions of protein\u2013ligand binding poses.<\/jats:p>","DOI":"10.1186\/s13321-021-00560-w","type":"journal-article","created":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T17:20:09Z","timestamp":1634404809000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["The impact of cross-docked poses on performance of machine learning classifier for protein\u2013ligand binding pose prediction"],"prefix":"10.1186","volume":"13","author":[{"given":"Chao","family":"Shen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueping","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junbo","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xujun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyang","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongsheng","family":"Cao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7227-2580","authenticated-orcid":false,"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,16]]},"reference":[{"key":"560_CR1","doi-asserted-by":"publisher","first-page":"3149","DOI":"10.1039\/C9CP06303J","volume":"22","author":"Z Wang","year":"2020","unstructured":"Wang Z, Sun H, Shen C et al (2020) Combined strategies in structure-based virtual screening. 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