{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T19:14:42Z","timestamp":1791486882707,"version":"4.3.4"},"reference-count":65,"publisher":"American Chemical Society (ACS)","issue":"14","license":[{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100005205","name":"Janssen Research and Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005205","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM148236"],"award-info":[{"award-number":["R35GM148236"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The quality of protein\u2013ligand binding affinity prediction is often limited by the accuracy of positioning the ligand correctly inside the binding site. However, pose accuracy is a secondary concern in high-throughput virtual screening, which is the application scenario in mind when most docking protocols are developed. On the other hand, similar protocols are also applied to position ligands in the binding pocket prior to free-energy calculations, and the accuracy of docking protocols is not well known in this case, especially when structures of analogues are available as templates to guide the docking, as is typical in lead optimization. Docking benchmarks typically focus on the ability of docking methods to generate poses with a low RMSD to crystal structures, but for physics-based affinity prediction methods, we also need the ability to identify potential alternate binding modes of a new ligand that might be viable. This is especially relevant for ligand modifications that break local symmetry, leading to multiple potential substituent orientations, such as substitutions of phenyl rings. Here, our focus is on assessment of pose prediction methods when the bound structure of a reference ligand is known (typical in structure-based drug design) and the likely binding mode(s) of a related compound are needed, and we focus on cases where the new compound has multiple potential binding modes. To assess templated docking protocols on their ability to identify binding modes when starting from a solid reference structure, we collected a set of 60 complex structures from the PDB that have more than one ligand binding mode \u2013 shown in the PDB records as alternative locations in the ligand. Our results suggest success rates of only 30\u201350% for finding alternative binding modes, which are modest compared to benchmarks of the same docking programs on the Astex diverse set (70\u201390% success rates). Overall, we conclude that docking methods would benefit from further tuning or improvement to become more effective in lead optimization.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c00356","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T23:54:07Z","timestamp":1784246047000},"page":"8269-8283","source":"Crossref","is-referenced-by-count":1,"title":["Benchmarking Docking Protocols on Predicting Alternative\nBinding Modes"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6518-681X","authenticated-orcid":true,"given":"Alz\u030cbeta","family":"Kubincova\u0301","sequence":"first","affiliation":[{"name":"University of California, Irvine , , , ,","place":["Irvine, California, United States, 92697"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7120-3540","authenticated-orcid":true,"given":"Su\u0308leyman Selim","family":"C\u0327inarog\u030clu","sequence":"additional","affiliation":[{"name":"Ege University , , ,","place":["Bornova, Tu\u0308rkiye, 35040"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianna","family":"Ongsioco","sequence":"additional","affiliation":[{"name":"University of California, Irvine , , , ,","place":["Irvine, California, United States, 92697"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David F.","family":"Hahn","sequence":"additional","affiliation":[{"name":"Janssen Research and Development, Janssen Pharmaceuticals N. V. , , Turnhoutseweg 30 , ,","place":["Beerse, Belgium, 2340"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6761-7780","authenticated-orcid":true,"given":"Vytautas","family":"Gapsys","sequence":"additional","affiliation":[{"name":"Janssen Research and Development, Janssen Pharmaceuticals N. V. , , Turnhoutseweg 30 , ,","place":["Beerse, Belgium, 2340"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4801-1644","authenticated-orcid":true,"given":"Gary","family":"Tresadern","sequence":"additional","affiliation":[{"name":"Janssen Research and Development, Janssen Pharmaceuticals N. V. , , Turnhoutseweg 30 , ,","place":["Beerse, Belgium, 2340"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1083-5533","authenticated-orcid":true,"given":"David L.","family":"Mobley","sequence":"additional","affiliation":[{"name":"University of California, Irvine , , , ,","place":["Irvine, California, United States, 92697"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"key":"2026072709082005000_cit1","doi-asserted-by":"publisher","first-page":"18378","DOI":"10.33011\/livecoms.2.1.18378","article-title":"Best Practices\nfor Alchemical Free Energy Calculations\n[Article v1.0]","volume":"2","author":"Mey","year":"2020","journal-title":"Living J. Comput. Mol. 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Pharmacol"},{"key":"2026072709082005000_cit4","doi-asserted-by":"publisher","first-page":"13384","DOI":"10.3390\/molecules200713384","article-title":"Molecular\nDocking and Structure-Based Drug Design Strategies","volume":"20","author":"Ferreira","year":"2015","journal-title":"Molecules"},{"key":"2026072709082005000_cit5","doi-asserted-by":"publisher","DOI":"10.1002\/minf.202400305","article-title":"Ultra-Large\nVirtual Screening: Definition, Recent Advances, and Challenges in\nDrug Design","volume":"44","author":"Corre\u0302a Veri\u0301ssimo","year":"2025","journal-title":"Mol. Inf."},{"key":"2026072709082005000_cit6","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1038\/s41586-023-05905-z","article-title":"Computational Approaches Streamlining Drug Discovery","volume":"616","author":"Sadybekov","year":"2023","journal-title":"Nature"},{"key":"2026072709082005000_cit7","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1002\/prot.20088","article-title":"A Detailed\nComparison of Current\nDocking and Scoring Methods on Systems of Pharmaceutical Relevance","volume":"56","author":"Perola","year":"2004","journal-title":"Proteins: Struct., Funct., Bioinf"},{"key":"2026072709082005000_cit8","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1021\/jm049798d","article-title":"Comparison\nof Automated Docking Programs as Virtual Screening Tools","volume":"48","author":"Cummings","year":"2005","journal-title":"J. Med. 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Inf.\nModel"},{"key":"2026072709082005000_cit15","doi-asserted-by":"publisher","first-page":"11183","DOI":"10.1021\/acs.jmedchem.8b01292","article-title":"qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like\nMolecules in X-Ray Electron Density Maps","volume":"61","author":"van Zundert","year":"2018","journal-title":"J.\nMed. Chem"},{"key":"2026072709082005000_cit16","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1016\/j.str.2009.02.010","article-title":"Binding of Small-Molecule Ligands to Proteins: \u201cWhat\nYou See\u201d Is Not Always \u201cWhat You Get\u201d","volume":"17","author":"Mobley","year":"2009","journal-title":"Structure"},{"key":"2026072709082005000_cit17","doi-asserted-by":"publisher","first-page":"2670","DOI":"10.1021\/acs.jctc.5b00214","article-title":"How To Deal with Multiple Binding\nPoses in Alchemical Relative Protein\u2013Ligand\nBinding Free Energy Calculations","volume":"11","author":"Kaus","year":"2015","journal-title":"J. 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Theory\nComput"},{"key":"2026072709082005000_cit22","first-page":"177","article-title":"Computational\nApproaches for Understanding Dynamical Systems: Protein Folding and\nAssembly","volume-title":"Progress in Molecular Biology\nand Translational Science","author":"Liao","year":"2020"},{"key":"2026072709082005000_cit23","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1021\/acs.jcim.9b01118","article-title":"Impact of Different\nAutomated Binding Pose Generation Approaches on Relative Binding Free\nEnergy Simulations","volume":"60","author":"Cappel","year":"2020","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit24","doi-asserted-by":"publisher","first-page":"8859","DOI":"10.1021\/acs.jcim.4c01223","article-title":"Input Pose\nIs Key to Performance of Free Energy Perturbation: Benchmarking with\nMonoacylglycerol Lipase","volume":"64","author":"Ohadi","year":"2024","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit25","doi-asserted-by":"publisher","first-page":"6927","DOI":"10.1021\/acs.jcim.5c00947","article-title":"Quantification\nof the Impact of Structure\nQuality on Predicted Binding Free Energy Accuracy","volume":"65","author":"Behera","year":"2025","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit26","doi-asserted-by":"publisher","first-page":"4890","DOI":"10.1016\/j.bmc.2016.07.044","article-title":"Blinded Predictions\nof Binding Modes and Energies of HSP90-\u03b1 Ligands\nfor the 2015 D3R Grand Challenge","volume":"24","author":"Mey","year":"2016","journal-title":"Bioorg. Med.\nChem"},{"key":"2026072709082005000_cit27","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/s42004-023-00859-9","article-title":"Automated Relative Binding Free Energy Calculations\nfrom SMILES to \u0394\u0394G","volume":"6","author":"Moore","year":"2023","journal-title":"Commun. Chem"},{"key":"2026072709082005000_cit28","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1007\/s10822-014-9723-5","article-title":"Blind Prediction\nof HIV Integrase Binding from the SAMPL4 Challenge","volume":"28","author":"Mobley","year":"2014","journal-title":"J. Comput.-Aided Mol. Des"},{"key":"2026072709082005000_cit29","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1007\/s10822-013-9702-2","article-title":"Combining in\nSilico and in Cerebro Approaches for Virtual Screening and Pose Prediction\nin SAMPL4","volume":"28","author":"Voet","year":"2014","journal-title":"J. Comput.-Aided Mol. Des"},{"key":"2026072709082005000_cit30","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/s42004-023-01019-9","article-title":"The Maximal and Current Accuracy\nof Rigorous Protein-Ligand Binding Free Energy Calculations","volume":"6","author":"Ross","year":"2023","journal-title":"Commun. Chem"},{"key":"2026072709082005000_cit31","doi-asserted-by":"publisher","first-page":"230901","DOI":"10.1063\/1.4769292","article-title":"Perspective:\nAlchemical Free Energy Calculations for\nDrug Discovery","volume":"137","author":"Mobley","year":"2012","journal-title":"J. Chem. Phys"},{"key":"2026072709082005000_cit32","doi-asserted-by":"publisher","first-page":"3812","DOI":"10.1021\/acs.jcim.4c00071","article-title":"FEP Augmentation as a Means to Solve Data Paucity Problems\nfor Machine Learning in Chemical Biology","volume":"64","author":"Burger","year":"2024","journal-title":"J.\nChem. Inf. Model"},{"key":"2026072709082005000_cit33","doi-asserted-by":"publisher","first-page":"2573","DOI":"10.1021\/acs.jcim.3c00100","article-title":"Modeling with\nAlternate\nLocations in X-ray Protein Structures","volume":"63","author":"Gutermuth","year":"2023","journal-title":"J. Chem.\nInf. Model"},{"key":"2026072709082005000_cit34","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1038\/s41597-024-03595-4","article-title":"A Dataset of Alternately Located\nSegments in Protein Crystal Structures","volume":"11","author":"Rosenberg","year":"2024","journal-title":"Sci.\nData"},{"key":"2026072709082005000_cit35","doi-asserted-by":"publisher","first-page":"2990","DOI":"10.1021\/acs.jctc.6b00201","article-title":"Prediction\nof Protein\u2013Ligand\nBinding Poses via a Combination of Induced Fit Docking and Metadynamics\nSimulations","volume":"12","author":"Clark","year":"2016","journal-title":"J. Chem. Theory Comput"},{"key":"2026072709082005000_cit36","doi-asserted-by":"publisher","first-page":"6209","DOI":"10.1021\/acs.jcim.2c01142","article-title":"Open Binding Pose\nMetadynamics: An Effective Approach\nfor the Ranking of Protein\u2013Ligand Binding Poses","volume":"62","author":"Lukauskis","year":"2022","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit37","doi-asserted-by":"publisher","first-page":"2044","DOI":"10.1021\/acs.jcim.0c00025","article-title":"Improving\nConformer\nGeneration for Small Rings and Macrocycles Based on Distance Geometry\nand Experimental Torsional-Angle Preferences","volume":"60","author":"Wang","year":"2020","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit38","doi-asserted-by":"publisher","first-page":"1893","DOI":"10.1021\/ci300604z","article-title":"Lessons Learned\nin Empirical Scoring\nwith Smina from the CSAR 2011 Benchmarking Exercise","volume":"53","author":"Koes","year":"2013","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit39","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1021\/acs.jctc.0c01006","article-title":"Accelerating AutoDock4 with GPUs and Gradient-Based Local Search","volume":"17","author":"Santos-Martins","year":"2021","journal-title":"J. Chem. 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Biol"},{"key":"2026072709082005000_cit41","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/11839088_22","article-title":"PLANTS: Application\nof Ant Colony Optimization to Structure-Based Drug Design","volume-title":"Ant Colony Optimization and Swarm Intelligence","author":"Korb","year":"2006"},{"key":"2026072709082005000_cit42","unstructured":"Prilusky, J.\n          \n          OCA, a Browser-Database\nfor Protein Structure\/Function. 1996; http:\/\/oca.weizmann.ac.il Accessed\non 27 April 2026."},{"key":"2026072709082005000_cit43","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4792","article-title":"UCSF ChimeraX:\nTools for Structure\nBuilding and Analysis","volume":"32","author":"Meng","year":"2023","journal-title":"Protein Sci"},{"key":"2026072709082005000_cit44","unstructured":"QUACPAC.\n          \n          OpenEye, Cadence Molecular Sciences, 2026; http:\/\/www.eyesopen.com."},{"key":"2026072709082005000_cit45","doi-asserted-by":"publisher","first-page":"10024","DOI":"10.1021\/ja00051a040","article-title":"UFF, a\nFull Periodic Table Force Field for Molecular Mechanics and Molecular\nDynamics Simulations","volume":"114","author":"Rappe","year":"1992","journal-title":"J. Am. Chem. Soc"},{"key":"2026072709082005000_cit46","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1021\/ci800298z","article-title":"Empirical Scoring Functions for Advanced\nProtein-Ligand Docking with PLANTS","volume":"49","author":"Korb","year":"2009","journal-title":"J. Chem.\nInf. Model"},{"key":"2026072709082005000_cit47","doi-asserted-by":"publisher","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated\nDocking with Selective Receptor Flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem"},{"key":"2026072709082005000_cit48","doi-asserted-by":"publisher","first-page":"13045","DOI":"10.1021\/acs.jcim.5c02271","article-title":"Meeko: Molecule Parametrization\nand Software Interoperability for Docking and Beyond","volume":"65","author":"Santos-Martins","year":"2025","journal-title":"J. Chem. Inf. 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Sci"},{"key":"2026072709082005000_cit52","doi-asserted-by":"publisher","first-page":"1499","DOI":"10.1021\/ci2002318","article-title":"TFD: Torsion Fingerprints\nAs a New Measure To Compare Small Molecule Conformations","volume":"52","author":"Schulz-Gasch","year":"2012","journal-title":"J. Chem. Inf. Model"},{"key":"2026072709082005000_cit53","doi-asserted-by":"publisher","first-page":"2562","DOI":"10.1021\/acs.jcim.5b00654","article-title":"Better Informed Distance Geometry: Using What We Know\nTo Improve Conformation Generation","volume":"55","author":"Riniker","year":"2015","journal-title":"J. Chem.\nInf. Model"},{"key":"2026072709082005000_cit54","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1021\/jm030209y","article-title":"Lessons in\nMolecular Recognition: The Effects of Ligand and Protein Flexibility\non Molecular Docking Accuracy","volume":"47","author":"Erickson","year":"2004","journal-title":"J. Med. Chem"},{"key":"2026072709082005000_cit55","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1021\/ci300399w","article-title":"Consensus\nDocking: Improving the Reliability of Docking\nin a Virtual Screening Context","volume":"53","author":"Houston","year":"2013","journal-title":"J. Chem. Inf.\nModel"},{"key":"2026072709082005000_cit56","doi-asserted-by":"publisher","DOI":"10.1017\/qrd.2022.18","article-title":"Performance Evaluation\nof Flexible Macrocycle Docking in AutoDock","volume":"3","author":"Holcomb","year":"2022","journal-title":"QRB Discovery"},{"key":"2026072709082005000_cit57","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/0263-7855(93)87001-L","article-title":"Molecular Recognition\nUsing a Binary Genetic Search\nAlgorithm","volume":"11","author":"Payne","year":"1993","journal-title":"J. Mol. 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