forked from D-Net/dnet-hadoop
2 lines
33 KiB
JSON
2 lines
33 KiB
JSON
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"description": [{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "The \u03b2-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for \u03b1-helical membrane proteins, currently there is no freely available prediction method for \u03b2-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of \u03b2-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane \u03b2-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer."}], "format": [], "journal": {"issnPrinted": "0305-1048", "name": "Nucleic Acids Research", "vol": "32", "sp": "W400", "issnOnline": "1362-4962", "ep": "W404"}, "coverage": [], "externalReference": [], "publisher": {"value": "Oxford University Press (OUP)"}, "language": {"classid": "und", "classname": "Undetermined", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["10.1093/nar/gkh417", "2137095432", "od_______267::d7b061d3850b0beeeca60a79f7136378", "datacite____::5dd8c2e14d8585702131935d49f8203a", "userclaim___::5dd8c2e14d8585702131935d49f8203a"], "source": [{"value": "Crossref"}, {}, {"dataInfo": {"provenanceaction": {"classid": "user:claim", "classname": "Linked by user", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "Nucleic Acids Research"}], "dateofacceptance": {"value": "2004-07-01"}, "title": [{"qualifier": {"classid": "alternative title", "classname": "alternative title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "PRED-TMBB: a web server for predicting the topology of \u03b2-barrel outer membrane proteins"}, {"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "pred tmbb a web server for predicting the topology of \u03b2 barrel outer membrane proteins"}, {"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "PRED-TMBB: a web server for predicting the topology of -barrel outer membrane proteins"}]}
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"schemename": "dnet:review_levels"}, "hostedby": {"key": "10|openaire____::55045bd2a65019fd8e6741a755395c8c", "value": "Unknown Repository"}, "url": ["http://dx.doi.org/10.1093/nar/gkh417"], "distributionlocation": "", "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "user:claim", "classname": "Linked by user", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "2004-07-01"}, "collectedfrom": {"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2019-11-27T11:43:24Z", "fulltext": [], "description": [{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "The \u03b2-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for \u03b1-helical membrane proteins, currently there is no freely available prediction method for \u03b2-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of \u03b2-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane \u03b2-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer."}], "format": [], "journal": {"issnPrinted": "0305-1048", "name": "Nucleic Acids Research", "vol": "32", "sp": "W400", "issnOnline": "1362-4962", "ep": "W404"}, "coverage": [], "externalReference": [], "publisher": {"value": "Oxford University Press (OUP)"}, "language": {"classid": "und", "classname": "Undetermined", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["10.1093/nar/gkh417", "2137095432", "od_______267::d7b061d3850b0beeeca60a79f7136378", "datacite____::5dd8c2e14d8585702131935d49f8203a", "userclaim___::5dd8c2e14d8585702131935d49f8203a"], "source": [{"value": "Crossref"}, {}, {"dataInfo": {"provenanceaction": {"classid": "user:claim", "classname": "Linked by user", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "Nucleic Acids Research"}], "dateofacceptance": {"value": "2004-07-01"}, "title": [{"qualifier": {"classid": "alternative title", "classname": "alternative title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "PRED-TMBB: a web server for predicting the topology of \u03b2-barrel outer membrane proteins"}, {"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "pred tmbb a web server for predicting the topology of \u03b2 barrel outer membrane proteins"}, {"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "PRED-TMBB: a web server for predicting the topology of -barrel outer membrane proteins"}]} |