{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T07:22:29Z","timestamp":1784618549555,"version":"3.55.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T00:00:00Z","timestamp":1659052800000},"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\/501100007300","name":"China Medical University","doi-asserted-by":"publisher","award":["CMU110-ASIA-07"],"award-info":[{"award-number":["CMU110-ASIA-07"]}],"id":[{"id":"10.13039\/501100007300","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>MIB2 (metal ion-binding) attempts to overcome the limitation of structure-based prediction approaches, with many proteins lacking a solved structure. MIB2 also offers more accurate prediction performance and more metal ion types.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>MIB2 utilizes both the (PS)2 method and the AlphaFold Protein Structure Database to acquire predicted structures to perform metal ion docking and predict binding residues. MIB2 offers marked improvements over MIB by collecting more MIB residue templates and using the metal ion type-specific scoring function. It offers a total of 18 types of metal ions for binding site predictions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Freely available on the web at http:\/\/bioinfo.cmu.edu.tw\/MIB2\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac534","type":"journal-article","created":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T15:09:30Z","timestamp":1659107370000},"page":"4428-4429","source":"Crossref","is-referenced-by-count":150,"title":["MIB2: metal ion-binding site prediction and modeling server"],"prefix":"10.1093","volume":"38","author":[{"given":"Chih-Hao","family":"Lu","sequence":"first","affiliation":[{"name":"The Ph.D. Program of Biotechnology and Biomedical industry, China Medical University , Taichung 404333, Taiwan"},{"name":"Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University , Hsinchu 300193, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5844-8428","authenticated-orcid":false,"given":"Chih-Chieh","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Medical Science and Technology, National Sun Yat-sen University , Kaohsiung 804201, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chin-Sheng","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Information Engineering and Computer Science, Feng Chia University , Taichung 407102, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yen-Yi","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Public Health, China Medical University , Taichung 406040, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Jun","family":"Liu","sequence":"additional","affiliation":[{"name":"The Ph.D. Program of Biotechnology and Biomedical industry, China Medical University , Taichung 404333, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sung-Tai","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, China Medical University Hospital , Taichung 404332, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1998-3310","authenticated-orcid":false,"given":"Yu-Feng","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Science and Biotechnology, Asia University , Taichung 413305, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,7,29]]},"reference":[{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"6214","DOI":"10.1002\/anie.201813576","article-title":"A simple approach to design proteins for the sustainable synthesis of metal nanoclusters","volume":"58","author":"Aires","year":"2019","journal-title":"Angew. Chem. Int. Ed. Engl"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1093\/bioinformatics\/bth095","article-title":"A hint to search for metalloproteins in gene banks","volume":"20","author":"Andreini","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1186\/1471-2105-10-366","article-title":"(PS)2-v2: template-based protein structure prediction server","volume":"10","author":"Chen","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"4478","DOI":"10.1039\/C6TB03295H","article-title":"Understanding the functional properties of bio-inorganic nanoflowers as biocatalysts by deciphering the metal-binding sites of enzymes","volume":"5","author":"Escobar","year":"2017","journal-title":"J. Mater. Chem. B"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"3260","DOI":"10.1093\/bioinformatics\/btw396","article-title":"Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals","volume":"32","author":"Hu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1021\/acs.jcim.6b00407","article-title":"MIB: metal ion-binding site prediction and docking server","volume":"56","author":"Lin","year":"2016","journal-title":"J. Chem. Inf. Model"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1002\/prot.20904","article-title":"The fragment transformation method to detect the protein structural motifs","volume":"63","author":"Lu","year":"2006","journal-title":"Proteins"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.ab.2018.11.009","article-title":"MIonSite: ligand-specific prediction of metal ion-binding sites via enhanced AdaBoost algorithm with protein sequence information","volume":"566","author":"Qiao","year":"2019","journal-title":"Anal. Biochem"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1021\/acs.jcim.0c00827","article-title":"BioMetAll: identifying metal-binding sites in proteins from backbone preorganization","volume":"61","author":"Sanchez-Aparicio","year":"2021","journal-title":"J. Chem. Inf. Model"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"9167","DOI":"10.1021\/bi0106742","article-title":"Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding","volume":"40","author":"Xie","year":"2001","journal-title":"Biochemistry"},{"key":"2023041408371054800_","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1109\/TCBB.2013.104","article-title":"Designing template-free predictor for targeting protein-ligand binding sites with classifier ensemble and spatial clustering","volume":"10","author":"Yu","year":"2013","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac534\/45249838\/btac534.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/18\/4428\/49884990\/btac534.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/18\/4428\/49884990\/btac534.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,25]],"date-time":"2023-11-25T03:52:47Z","timestamp":1700884367000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/18\/4428\/6651835"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,7,29]]},"references-count":12,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2022,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac534","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,9,15]]},"published":{"date-parts":[[2022,7,29]]}}}