{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T17:41:03Z","timestamp":1781545263480,"version":"3.54.5"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T00:00:00Z","timestamp":1602633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30 DA035778A1"],"award-info":[{"award-number":["P30 DA035778A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Delineating the fingerprint or feature vector of a receptor\/protein will facilitate the structural and biological studies, as well as the rational design and development of drugs with high affinities and selectivity. However, protein is complicated by its different functional regions that can bind to some of its protein partner(s), substrate(s), orthosteric ligand(s) or allosteric modulator(s) where cogent methods like molecular fingerprints do not work well. We here elaborate a scoring-function-based computing protocol Molecular Complex Characterizing System to help characterize the binding feature of protein\u2013ligand complexes. Based on the reported receptor-ligand interactions, we first quantitate the energy contribution of each individual residue which may be an alternative of MD-based energy decomposition. We then construct a vector for the energy contribution to represent the pattern of the ligand recognition at a receptor and qualitatively analyze the matching level with other receptors. Finally, the energy contribution vector is explored for extensive use in similarity and clustering. The present work provides a new approach to cluster proteins, a perspective counterpart for determining the protein characteristics in the binding, and an advanced screening technique where molecular docking is applicable.<\/jats:p>","DOI":"10.1093\/bib\/bbaa239","type":"journal-article","created":{"date-parts":[[2020,8,28]],"date-time":"2020-08-28T19:11:37Z","timestamp":1598641897000},"source":"Crossref","is-referenced-by-count":22,"title":["MCCS, a novel characterization method for protein\u2013ligand complex"],"prefix":"10.1093","volume":"22","author":[{"given":"Maozi","family":"Chen","sequence":"first","affiliation":[{"name":"University of Pittsburgh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6533-8932","authenticated-orcid":false,"given":"Zhiwei","family":"Feng","sequence":"additional","affiliation":[{"name":"University of Pittsburgh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyi","family":"Wang","sequence":"additional","affiliation":[{"name":"University of Pittsburgh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Lin","sequence":"additional","affiliation":[{"name":"University of Pittsburgh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang-Qun","family":"Xie","sequence":"additional","affiliation":[{"name":"University of Pittsburgh"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,14]]},"reference":[{"key":"2021072112190721600_ref1","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1208\/s12248-015-9776-y","article-title":"Computational advances for the development of allosteric modulators and bitopic ligands in G protein-coupled receptors","volume":"17","author":"Feng","year":"2015","journal-title":"AAPS J"},{"key":"2021072112190721600_ref2","doi-asserted-by":"crossref","first-page":"7393","DOI":"10.1021\/acs.jmedchem.7b00696","article-title":"A simple representation of three-dimensional molecular structure","volume":"60","author":"Axen","year":"2017","journal-title":"J Med Chem"},{"key":"2021072112190721600_ref3","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1021\/acs.jcim.8b00623","article-title":"DAKB-GPCRs: an integrated computational platform for drug abuse related GPCRs","volume":"59","author":"Chen","year":"2019","journal-title":"J Chem Inf Model"},{"key":"2021072112190721600_ref4","doi-asserted-by":"crossref","first-page":"232a","DOI":"10.1016\/j.bpj.2017.11.1289","article-title":"Molecular basis for the functionality of \u03b3-secretase inferred from structure-based modeling and druggability simulations","volume":"114","author":"Lee","year":"2018","journal-title":"Biophys J"},{"key":"2021072112190721600_ref5","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1021\/ci5002718","article-title":"Modeling, molecular dynamics simulation, and mutation validation for structure of cannabinoid receptor 2 based on known crystal structures of GPCRs","volume":"54","author":"Feng","year":"2014","journal-title":"J Chem Inf Model"},{"key":"2021072112190721600_ref6","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1016\/j.cell.2020.01.007","article-title":"Cryo-EM structure of the human cannabinoid receptor CB2-Gi Signaling complex","volume":"180","author":"Xing","year":"2020","journal-title":"Cell"},{"key":"2021072112190721600_ref7","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1007\/s10822-015-9833-8","article-title":"Models of protein\u2013ligand crystal structures: trust, but verify","volume":"29","author":"Deller","year":"2015","journal-title":"J Comput Aided Mol Des"},{"key":"2021072112190721600_ref8","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J Comput Chem"},{"key":"2021072112190721600_ref9","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J Comput Chem"},{"key":"2021072112190721600_ref10","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","article-title":"Glide: a new approach for rapid, accurate docking and scoring. 1. 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