{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Okimoto N"],"funding":["Japan Society for the Promotion of Science"],"pagination":["4475-4485"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6641631"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["3(4)"],"pubmed_abstract":["In computational drug discovery, ranking a series of compound analogues in the order that is consistent with the experimental binding affinities remains a challenge. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics (MM)-based force fields, although they cannot completely describe protein-ligand interactions. By contrast, quantum mechanics (QM) calculations play an important role in understanding the protein-ligand interactions; however, their huge computational costs hinder their application in drug discovery. In this study, we have evaluated the ability to rank the binding affinities of tankyrase 2 ligands by combining both MM and QM calculations. Our computational approach uses the protein-ligand binding energies obtained from"],"journal":["ACS omega"],"pubmed_title":["Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein-Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors."],"pmcid":["PMC6641631"],"funding_grant_id":["26610120","22790122","16KT0168"],"pubmed_authors":["Taiji M","Okimoto N","Otsuka T","Hirano Y"],"additional_accession":[]},"is_claimable":false,"name":"Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein-Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors.","description":"In computational drug discovery, ranking a series of compound analogues in the order that is consistent with the experimental binding affinities remains a challenge. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics (MM)-based force fields, although they cannot completely describe protein-ligand interactions. By contrast, quantum mechanics (QM) calculations play an important role in understanding the protein-ligand interactions; however, their huge computational costs hinder their application in drug discovery. In this study, we have evaluated the ability to rank the binding affinities of tankyrase 2 ligands by combining both MM and QM calculations. Our computational approach uses the protein-ligand binding energies obtained from","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018 Apr","modification":"2026-05-07T05:28:20.167Z","creation":"2025-05-18T13:15:33.962Z"},"accession":"S-EPMC6641631","cross_references":{"pubmed":["31458673"],"doi":["10.1021/acsomega.8b00175"]}}