{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T18:44:43Z","timestamp":1773859483034,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2018,4,26]],"date-time":"2018-04-26T00:00:00Z","timestamp":1524700800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003549","name":"Hungarian Scientific Research Fund","doi-asserted-by":"publisher","award":["K119287"],"award-info":[{"award-number":["K119287"]}],"id":[{"id":"10.13039\/501100003549","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003825","name":"Hungarian Academy of Sciences","doi-asserted-by":"publisher","award":["LP2012\/35"],"award-info":[{"award-number":["LP2012\/35"]}],"id":[{"id":"10.13039\/501100003825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003825","name":"Hungarian Academy of Sciences","doi-asserted-by":"publisher","award":["FIEK_16-1-2016-0005"],"award-info":[{"award-number":["FIEK_16-1-2016-0005"]}],"id":[{"id":"10.13039\/501100003825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012550","name":"National Research, Development and Innovation Fund","doi-asserted-by":"crossref","award":["\u00daNKP-16-2_VBK-016"],"award-info":[{"award-number":["\u00daNKP-16-2_VBK-016"]}],"id":[{"id":"10.13039\/501100012550","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005881","name":"Ministry of Human Resources","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005881","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Transmembrane proteins (TMPs) are crucial in the life of the cells. As they have special properties, their structure is hard to determine\u2013\u2013the PDB database consists of 2% TMPs, despite the fact that they are predicted to make up to 25% of the human proteome. Crystallization prediction methods were developed to aid the target selection for structure determination, however, there is a need for a TMP specific service.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present TMCrys, a crystallization prediction method that surpasses existing prediction methods in performance thanks to its specialization for TMPs. We expect TMCrys to improve target selection of TMPs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/brgenzim\/tmcrys<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty342","type":"journal-article","created":{"date-parts":[[2018,4,25]],"date-time":"2018-04-25T19:59:04Z","timestamp":1524686344000},"page":"3126-3130","source":"Crossref","is-referenced-by-count":9,"title":["TMCrys: predict propensity of success for transmembrane protein crystallization"],"prefix":"10.1093","volume":"34","author":[{"given":"Julia K","family":"Varga","sequence":"first","affiliation":[{"name":"\u2018Momentum\u2019 Membrane Protein Bioinformatics Research Group, Institute of Enzymology, Research Center of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary"}]},{"given":"G\u00e1bor E","family":"Tusn\u00e1dy","sequence":"additional","affiliation":[{"name":"\u2018Momentum\u2019 Membrane Protein Bioinformatics Research Group, Institute of Enzymology, Research Center of Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary"}]}],"member":"286","published-online":{"date-parts":[[2018,4,26]]},"reference":[{"key":"2023012704181051800_bty342-B1","doi-asserted-by":"crossref","first-page":"52","DOI":"10.3109\/09687688.2012.703703","article-title":"Overexpression of membrane proteins in mammalian cells for structural studies","volume":"30","author":"Andr\u00e9ll","year":"2013","journal-title":"Mol. Membr. Biol"},{"key":"2023012704181051800_bty342-B2","doi-asserted-by":"crossref","first-page":"e72368","DOI":"10.1371\/journal.pone.0072368","article-title":"SCMCRYS: predicting protein crystallization using an ensemble scoring card method with estimating propensity scores of P-collocated amino acid pairs","volume":"8","author":"Charoenkwan","year":"2013","journal-title":"PLoS One"},{"key":"2023012704181051800_bty342-B3","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1093\/bioinformatics\/bth300","article-title":"TargetDB: a target registration database for structural genomics projects","volume":"20","author":"Chen","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012704181051800_bty342-B4","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.bbrc.2007.02.040","article-title":"Prediction of protein crystallization using collocation of amino acid pairs","volume":"355","author":"Chen","year":"2007","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023012704181051800_bty342-B5","author":"Chen","year":"2017"},{"key":"2023012704181051800_bty342-B6","author":"Chen","year":"2016"},{"key":"2023012704181051800_bty342-B7","doi-asserted-by":"crossref","first-page":"W408","DOI":"10.1093\/nar\/gkv451","article-title":"CCTOP: a Consensus Constrained TOPology prediction web server","volume":"43","author":"Dobson","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012704181051800_bty342-B8","doi-asserted-by":"crossref","first-page":"31.","DOI":"10.1186\/s13062-015-0061-x","article-title":"The human transmembrane proteome","volume":"10","author":"Dobson","year":"2015","journal-title":"Biol. Direct"},{"key":"2023012704181051800_bty342-B9","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012704181051800_bty342-B10","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s10969-011-9106-2","article-title":"The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J. Struct","volume":"12","author":"Gabanyi","year":"2011","journal-title":"Funct. Genomics"},{"key":"2023012704181051800_bty342-B11","doi-asserted-by":"crossref","first-page":"M111.007930","DOI":"10.1074\/mcp.M111.007930","article-title":"Physiological response to membrane protein overexpression in E. coli","volume":"10","author":"Gubellini","year":"2011","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012704181051800_bty342-B12","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.cell.2016.12.030","article-title":"structural titration of Slo2.2, a Na+-dependent K+ channel","volume":"168","author":"Hite","year":"2017","journal-title":"Cell"},{"key":"2023012704181051800_bty342-B13","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nrd892","article-title":"The druggable genome","volume":"1","author":"Hopkins","year":"2002","journal-title":"Nat. Rev. Drug Discov"},{"key":"2023012704181051800_bty342-B14","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1107\/S1399004713032070","article-title":"Improving the chances of successful protein structure determination with a random forest classifier","volume":"70","author":"Jahandideh","year":"2014","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr"},{"key":"2023012704181051800_bty342-B15","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1093\/nar\/27.1.368","article-title":"AAindex: amino acid index database","volume":"27","author":"Kawashima","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023012704181051800_bty342-B16","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-60327-058-8","volume-title":"Structural Proteomics","author":"Kobe","year":"2008"},{"key":"2023012704181051800_bty342-B17","doi-asserted-by":"crossref","first-page":"D524","DOI":"10.1093\/nar\/gks1169","article-title":"PDBTM: protein Data Bank of transmembrane proteins after 8 years","volume":"41","author":"Kozma","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012704181051800_bty342-B18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v028.i05","article-title":"Building predictive models in R using the caret package","volume":"28","author":"Kuhn","year":"2008","journal-title":"J. Stat. Software"},{"key":"2023012704181051800_bty342-B19","author":"Kuhn","year":"2017"},{"key":"2023012704181051800_bty342-B20","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1472-6807-9-50","article-title":"CRYSTALP2: sequence-based protein crystallization propensity prediction","volume":"9","author":"Kurgan","year":"2009","journal-title":"BMC Struct. Biol"},{"key":"2023012704181051800_bty342-B21","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s10969-010-9094-7","article-title":"The New York consortium on membrane protein structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins","volume":"11","author":"Love","year":"2010","journal-title":"J. Struct. Funct. Genomics"},{"key":"2023012704181051800_bty342-B22","doi-asserted-by":"crossref","first-page":"2597","DOI":"10.1007\/s00018-006-6252-y","article-title":"Structural genomics for membrane proteins","volume":"63","author":"Lundstrom","year":"2006","journal-title":"Cell. Mol. Life Sci"},{"key":"2023012704181051800_bty342-B23","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1002\/prot.21605","article-title":"Predicting experimental properties of integral membrane proteins by a naive Bayes approach","volume":"70","author":"Martin-Galiano","year":"2008","journal-title":"Proteins Struct. Funct. Genet"},{"key":"2023012704181051800_bty342-B24","first-page":"53","volume-title":"Codon Optimizing for Increased Membrane Protein Production: A Minimalist Approach","author":"Mirzadeh","year":"2016"},{"key":"2023012704181051800_bty342-B25","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.bbamem.2013.07.010","article-title":"Membrane protein structure determination - the next generation","volume":"1838","author":"Moraes","year":"2014","journal-title":"Biochim. Biophys. Acta"},{"key":"2023012704181051800_bty342-B26","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nmeth.3694","article-title":"The development of cryo-EM into a mainstream structural biology technique","volume":"13","author":"Nogales","year":"2016","journal-title":"Nat. Methods"},{"key":"2023012704181051800_bty342-B27","author":"Olson","year":"2017"},{"key":"2023012704181051800_bty342-B28","doi-asserted-by":"crossref","first-page":"4005","DOI":"10.1016\/j.febslet.2006.06.015","article-title":"A normalised scale for structural genomics target ranking: the OB-Score","volume":"580","author":"Overton","year":"2006","journal-title":"FEBS Lett"},{"key":"2023012704181051800_bty342-B29","doi-asserted-by":"crossref","first-page":"51.","DOI":"10.1186\/1472-6807-9-51","article-title":"A generic method for assignment of reliability scores applied to solvent accessibility predictions","volume":"9","author":"Petersen","year":"2009","journal-title":"BMC Struct. Biol"},{"key":"2023012704181051800_bty342-B30","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1023\/A:1007601015854","article-title":"Robust classification for imprecise environments","volume":"42","author":"Provost","year":"2001","journal-title":"Mach. Learn"},{"key":"2023012704181051800_bty342-B31","first-page":"4913","author":"Saladi","year":"2018"},{"key":"2023012704181051800_bty342-B32","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.cbpa.2013.04.002","article-title":"Stabilizing membrane proteins through protein engineering","volume":"17","author":"Scott","year":"2013","journal-title":"Curr. Opin. Chem. Biol"},{"key":"2023012704181051800_bty342-B33","doi-asserted-by":"crossref","first-page":"3403","DOI":"10.1093\/bioinformatics\/btm477","article-title":"XtalPred: a web server for prediction of protein crystallizability","volume":"23","author":"Slabinski","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012704181051800_bty342-B34","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gkw939","article-title":"TSTMP: target selection for structural genomics of human transmembrane proteins","volume":"45","author":"Varga","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012704181051800_bty342-B35","doi-asserted-by":"crossref","DOI":"10.1385\/1592598900","volume-title":"The Proteomics Protocols Handbook","author":"Walker","year":"2005"},{"key":"2023012704181051800_bty342-B36","doi-asserted-by":"crossref","first-page":"e105902.","DOI":"10.1371\/journal.pone.0105902","article-title":"PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection","volume":"9","author":"Wang","year":"2014","journal-title":"PLoS One"},{"key":"2023012704181051800_bty342-B37","doi-asserted-by":"crossref","first-page":"21383","DOI":"10.1038\/srep21383","article-title":"Crysalis: an integrated server for computational analysis and design of protein crystallization","volume":"6","author":"Wang","year":"2016","journal-title":"Sci. Rep"},{"key":"2023012704181051800_bty342-B38","first-page":"1","article-title":"Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity","volume":"7","author":"Wang","year":"2017","journal-title":"Brief. Bioinform"},{"key":"2023012704181051800_bty342-B39","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1093\/bioinformatics\/btv042","article-title":"protr\/ProtrWeb: r package and web server for generating various numerical representation schemes of protein sequences","volume":"31","author":"Xiao","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3126\/48919293\/bioinformatics_34_18_3126.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3126\/48919293\/bioinformatics_34_18_3126.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T04:40:20Z","timestamp":1674794420000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/18\/3126\/4987146"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,26]]},"references-count":39,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2018,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty342","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,15]]},"published":{"date-parts":[[2018,4,26]]}}}