[ { "key": "Z87HQZU7", "version": 70, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/Z87HQZU7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/Z87HQZU7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/UTT3UB2V", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "Z87HQZU7", "version": 70, "parentItem": "UTT3UB2V", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2017-05-03T19:25:32Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646828/pdf/pone.0061122.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Borley et al. - 2013 - Evaluation and Use of In-Silico Structure-Based Ep.pdf", "md5": "6aab937b033d5f351fe28f6642ff93cc", "mtime": 1493839694000, "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:25:32Z", "dateModified": "2017-05-03T19:28:14Z" } }, { "key": "X8352QPG", "version": 70, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/X8352QPG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/X8352QPG", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/3N7K4GZG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "X8352QPG", "version": 70, "parentItem": "3N7K4GZG", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2017-05-03T19:25:00Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679652/pdf/nihms733138.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Eren et al. - 2016 - Modeling of the rotavirus group C capsid predicts .pdf", "md5": "3857886b26bdc29f38aea440e569443a", "mtime": 1493839691000, "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:25:00Z", "dateModified": "2017-05-03T19:28:11Z" } }, { "key": "UTT3UB2V", "version": 68, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/UTT3UB2V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/UTT3UB2V", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Borley et al.", "parsedDate": "2013-05-07", "numChildren": 2 }, "data": { "key": "UTT3UB2V", "version": 68, "itemType": "journalArticle", "title": "Evaluation and Use of In-Silico Structure-Based Epitope Prediction with Foot-and-Mouth Disease Virus", "creators": [ { "creatorType": "author", "firstName": "Daryl W.", "lastName": "Borley" }, { "creatorType": "author", "firstName": "Mana", "lastName": "Mahapatra" }, { "creatorType": "author", "firstName": "David J.", "lastName": "Paton" }, { "creatorType": "author", "firstName": "Robert M.", "lastName": "Esnouf" }, { "creatorType": "author", "firstName": "David I.", "lastName": "Stuart" }, { "creatorType": "author", "firstName": "Elizabeth E.", "lastName": "Fry" } ], "abstractNote": "Understanding virus antigenicity is of fundamental importance for the development of better, more cross-reactive vaccines. However, as far as we are aware, no systematic work has yet been conducted using the 3D structure of a virus to identify novel epitopes. Therefore we have extended several existing structural prediction algorithms to build a method for identifying epitopes on the appropriate outer surface of intact virus capsids (which are structurally different from globular proteins in both shape and arrangement of multiple repeated elements) and applied it here as a proof of principle concept to the capsid of foot-and-mouth disease virus (FMDV). We have analysed how reliably several freely available structure-based B cell epitope prediction programs can identify already known viral epitopes of FMDV in the context of the viral capsid. To do this we constructed a simple objective metric to measure the sensitivity and discrimination of such algorithms. After optimising the parameters for five methods using an independent training set we used this measure to evaluate the methods. Individually any one algorithm performed rather poorly (three performing better than the other two) suggesting that there may be value in developing virus-specific software. Taking a very conservative approach requiring a consensus between all three top methods predicts a number of previously described antigenic residues as potential epitopes on more than one serotype of FMDV, consistent with experimental results. The consensus results identified novel residues as potential epitopes on more than one serotype. These include residues 190–192 of VP2 (not previously determined to be antigenic), residues 69–71 and 193–197 of VP3 spanning the pentamer-pentamer interface, and another region incorporating residues 83, 84 and 169–174 of VP1 (all only previously experimentally defined on serotype A). The computer programs needed to create a semi-automated procedure for carrying out this epitope prediction method are presented.", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "2013-5-7", "volume": "8", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS One", "DOI": "10.1371/journal.pone.0061122", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646828/", "accessDate": "2017-05-03T19:25:32Z", "PMID": "", "PMCID": "", "ISSN": "1932-6203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 23667434\nPMCID: PMC3646828", "tags": [], "collections": [ "4W2RHDGF" ], "relations": {}, "dateAdded": "2017-05-03T19:25:32Z", "dateModified": "2017-05-03T19:25:32Z" } }, { "key": "GS2ITI3E", "version": 68, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/GS2ITI3E", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/GS2ITI3E", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/UTT3UB2V", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } } }, "data": { "key": "GS2ITI3E", "version": 68, "parentItem": "UTT3UB2V", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2017-05-03T19:25:32Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646828/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:25:32Z", "dateModified": "2017-05-03T19:25:32Z" } }, { "key": "C4D7G85I", "version": 67, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/C4D7G85I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/C4D7G85I", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/3N7K4GZG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } } }, "data": { "key": "C4D7G85I", "version": 67, "parentItem": "3N7K4GZG", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2017-05-03T19:25:00Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679652/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:25:00Z", "dateModified": "2017-05-03T19:25:00Z" } }, { "key": "3N7K4GZG", "version": 67, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/3N7K4GZG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/3N7K4GZG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Eren et al.", "parsedDate": "2016-01", "numChildren": 2 }, "data": { "key": "3N7K4GZG", "version": 67, "itemType": "journalArticle", "title": "Modeling of the rotavirus group C capsid predicts a surface topology distinct from other rotavirus species", "creators": [ { "creatorType": "author", "firstName": "Elif", "lastName": "Eren" }, { "creatorType": "author", "firstName": "Kimberly", "lastName": "Zamuda" }, { "creatorType": "author", "firstName": "John T.", "lastName": "Patton" } ], "abstractNote": "Rotavirus C (RVC) causes sporadic gastroenteritis in adults and is an established enteric pathogen of swine. Because RVC strains grow poorly in cell culture, which hinders generation of virion-derived RVC triple-layered-particle (TLP) structures, we used the known Rotavirus A (RVA) capsid structure to model the human RVC (Bristol) capsid. Comparative analysis of RVA and RVC capsid proteins showed major differences at the VP7 layer, an important target region for vaccine development due to its antigenic properties. Our model predicted the presence of a surface extended loop in RVC, which could form a major antigenic site on the capsid. We analyzed variations in the glycosylation patterns among RV capsids and identified group specific conserved sites. In addition, our results showed a smaller RVC VP4 foot, which protrudes toward the intermediate VP6 layer, in comparison to that of RVA. Finally, our results showed major structural differences at the VP8* glycan recognition sites.", "publicationTitle": "Virology", "publisher": "", "place": "", "date": "2016-1", "volume": "487", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "150-162", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Virology", "DOI": "10.1016/j.virol.2015.10.017", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679652/", "accessDate": "2017-05-03T19:25:00Z", "PMID": "", "PMCID": "", "ISSN": "0042-6822", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 26524514\nPMCID: PMC4679652", "tags": [], "collections": [ "4W2RHDGF" ], "relations": {}, "dateAdded": "2017-05-03T19:25:00Z", "dateModified": "2017-05-03T19:25:00Z" } }, { "key": "9Z4SB7W5", "version": 66, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/9Z4SB7W5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/9Z4SB7W5", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/XZXWUIFA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "9Z4SB7W5", "version": 66, "parentItem": "XZXWUIFA", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2017-05-03T19:24:15Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227168/pdf/JIR2016-6760830.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Potocnakova et al. - 2016 - An Introduction to B-Cell Epitope Mapping and In S.pdf", "md5": "42db73e816fe1b28aca55845c0231d7e", "mtime": 1493839456000, "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:24:15Z", "dateModified": "2017-05-03T19:24:17Z" } }, { "key": "3PQ9HHH3", "version": 65, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/3PQ9HHH3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/3PQ9HHH3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/XZXWUIFA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } } }, "data": { "key": "3PQ9HHH3", "version": 65, "parentItem": "XZXWUIFA", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2017-05-03T19:24:15Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227168/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:24:15Z", "dateModified": "2017-05-03T19:24:15Z" } }, { "key": "XZXWUIFA", "version": 65, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/XZXWUIFA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/XZXWUIFA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Potocnakova et al.", "parsedDate": "2016", "numChildren": 2 }, "data": { "key": "XZXWUIFA", "version": 65, "itemType": "journalArticle", "title": "An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction", "creators": [ { "creatorType": "author", "firstName": "Lenka", "lastName": "Potocnakova" }, { "creatorType": "author", "firstName": "Mangesh", "lastName": "Bhide" }, { "creatorType": "author", "firstName": "Lucia Borszekova", "lastName": "Pulzova" } ], "abstractNote": "Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.", "publicationTitle": "Journal of Immunology Research", "publisher": "", "place": "", "date": "2016", "volume": "2016", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Immunol Res", "DOI": "10.1155/2016/6760830", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5227168/", "accessDate": "2017-05-03T19:24:15Z", "PMID": "", "PMCID": "", "ISSN": "2314-8861", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 28127568\nPMCID: PMC5227168", "tags": [], "collections": [ "4W2RHDGF" ], "relations": {}, "dateAdded": "2017-05-03T19:24:15Z", "dateModified": "2017-05-03T19:24:15Z" } }, { "key": "934UU4TB", "version": 64, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/934UU4TB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/934UU4TB", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/6CEG3MTU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "934UU4TB", "version": 64, "parentItem": "6CEG3MTU", "itemType": "attachment", "linkMode": "imported_url", "title": "ScienceDirect Full Text PDF", "accessDate": "2017-05-03T19:22:45Z", "url": "http://www.sciencedirect.com/science/article/pii/S0161589007007961/pdfft?md5=e9bf78e8082199586f8ce42ea1e941c4&pid=1-s2.0-S0161589007007961-main.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Rubinstein et al. - 2008 - Computational characterization of B-cell epitopes.pdf", "md5": "e1f46e4e9363f5658191b77c22196511", "mtime": 1493839373000, "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:22:45Z", "dateModified": "2017-05-03T19:22:53Z" } }, { "key": "PBVHFC82", "version": 64, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/PBVHFC82", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/PBVHFC82", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/6CEG3MTU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } } }, "data": { "key": "PBVHFC82", "version": 64, "parentItem": "6CEG3MTU", "itemType": "attachment", "linkMode": "imported_url", "title": "ScienceDirect Snapshot", "accessDate": "2017-05-03T19:22:45Z", "url": "http://www.sciencedirect.com/science/article/pii/S0161589007007961", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "S0161589007007961.html", "md5": "139e69b864dda3fbd0cae5b8a6edd2be", "mtime": 1493839367000, "tags": [], "relations": {}, "dateAdded": "2017-05-03T19:22:45Z", "dateModified": "2017-05-03T19:22:45Z" } }, { "key": "6CEG3MTU", "version": 63, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/6CEG3MTU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/6CEG3MTU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Rubinstein et al.", "parsedDate": "2008-07", "numChildren": 2 }, "data": { "key": "6CEG3MTU", "version": 63, "itemType": "journalArticle", "title": "Computational characterization of B-cell epitopes", "creators": [ { "creatorType": "author", "firstName": "Nimrod D.", "lastName": "Rubinstein" }, { "creatorType": "author", "firstName": "Itay", "lastName": "Mayrose" }, { "creatorType": "author", "firstName": "Dan", "lastName": "Halperin" }, { "creatorType": "author", "firstName": "Daniel", "lastName": "Yekutieli" }, { "creatorType": "author", "firstName": "Jonathan M.", "lastName": "Gershoni" }, { "creatorType": "author", "firstName": "Tal", "lastName": "Pupko" } ], "abstractNote": "Characterizing B-cell epitopes is a fundamental step for understanding the immunological basis of bio-recognition. To date, epitope analyses have either been based on limited structural data, or sequence data alone. In this study, our null hypothesis was that the surface of the antigen is homogeneously antigenic. To test this hypothesis, a large dataset of antibody–antigen complex structures, together with crystal structures of the native antigens, has been compiled. Computational methods were developed and applied to detect and extract physico-chemical, structural, and geometrical properties that may distinguish an epitope from the remaining antigen surface. Rigorous statistical inference was able to clearly reject the null hypothesis showing that epitopes are distinguished from the remaining antigen surface in properties such as amino acid preference, secondary structure composition, geometrical shape, and evolutionary conservation. Specifically, epitopes were found to be significantly enriched with tyrosine and tryptophan, and to show a general preference for charged and polar amino acids. Additionally, epitopes were found to show clear preference for residing on planar parts of the antigen that protrude from the surface, yet with a rugged surface shape at the atom level. The effects of complex formation on the structural properties of the antigen were also computationally characterized and it is shown that epitopes undergo compression upon antibody binding. This correlates with the finding that epitopes are enriched with unorganized secondary structure elements that render them flexible. Thus, this study extends the understanding of the underlying processes required for antibody binding, and reveals new aspects of the antibody–antigen interaction.", "publicationTitle": "Molecular Immunology", "publisher": "", "place": "", "date": "Julho 2008", "volume": "45", "issue": "12", "section": "", "partNumber": "", "partTitle": "", "pages": "3477-3489", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Molecular Immunology", "DOI": "10.1016/j.molimm.2007.10.016", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0161589007007961", "accessDate": "2017-05-03T19:22:45Z", "PMID": "", "PMCID": "", "ISSN": "0161-5890", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Antibody", "type": 1 }, { "tag": "Antigen", "type": 1 }, { "tag": "Epitope", "type": 1 }, { "tag": "Surface", "type": 1 } ], "collections": [ "4W2RHDGF" ], "relations": {}, "dateAdded": "2017-05-03T19:22:45Z", "dateModified": "2017-05-03T19:22:45Z" } }, { "key": "D38N3ZXH", "version": 61, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/D38N3ZXH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/D38N3ZXH", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/2C7SG2T9", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "D38N3ZXH", "version": 61, "parentItem": "2C7SG2T9", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2016-12-27T17:15:03Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648739/pdf/1471-2105-10-S1-S42.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Han et al. - 2009 - Predicting disordered regions in proteins using th.pdf", "md5": "91548362bc787a55b6cec751d6e47600", "mtime": 1491421112000, "tags": [], "relations": {}, "dateAdded": "2017-04-05T19:38:32Z", "dateModified": "2017-04-05T19:38:32Z" } }, { "key": "2K2NHS8K", "version": 60, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/2K2NHS8K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/2K2NHS8K", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/2C7SG2T9", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } } }, "data": { "key": "2K2NHS8K", "version": 60, "parentItem": "2C7SG2T9", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2016-12-27T17:15:03Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648739/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2017-04-05T19:38:32Z", "dateModified": "2017-04-05T19:38:32Z" } }, { "key": "2C7SG2T9", "version": 60, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/2C7SG2T9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/2C7SG2T9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Han et al.", "parsedDate": "2009-01-30", "numChildren": 2 }, "data": { "key": "2C7SG2T9", "version": 60, "itemType": "journalArticle", "title": "Predicting disordered regions in proteins using the profiles of amino acid indices", "creators": [ { "creatorType": "author", "firstName": "Pengfei", "lastName": "Han" }, { "creatorType": "author", "firstName": "Xiuzhen", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Zhi-Ping", "lastName": "Feng" } ], "abstractNote": "Background\nIntrinsically unstructured or disordered proteins are common and functionally important. Prediction of disordered regions in proteins can provide useful information for understanding protein function and for high-throughput determination of protein structures.\n\nResults\nIn this paper, algorithms are presented to predict long and short disordered regions in proteins, namely the long disordered region prediction algorithm DRaai-L and the short disordered region prediction algorithm DRaai-S. These algorithms are developed based on the Random Forest machine learning model and the profiles of amino acid indices representing various physiochemical and biochemical properties of the 20 amino acids.\n\nConclusion\nExperiments on DisProt3.6 and CASP7 demonstrate that some sets of the amino acid indices have strong association with the ordered and disordered status of residues. Our algorithms based on the profiles of these amino acid indices as input features to predict disordered regions in proteins outperform that based on amino acid composition and reduced amino acid composition, and also outperform many existing algorithms. Our studies suggest that the profiles of amino acid indices combined with the Random Forest learning model is an important complementary method for pinpointing disordered regions in proteins.", "publicationTitle": "BMC Bioinformatics", "publisher": "", "place": "", "date": "2009-1-30", "volume": "10", "issue": "Suppl 1", "section": "", "partNumber": "", "partTitle": "", "pages": "S42", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Bioinformatics", "DOI": "10.1186/1471-2105-10-S1-S42", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648739/", "accessDate": "2016-12-27T17:15:03Z", "PMID": "", "PMCID": "", "ISSN": "1471-2105", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 19208144\nPMCID: PMC2648739", "tags": [], "collections": [ "6EXCB4HX" ], "relations": {}, "dateAdded": "2017-04-05T19:38:32Z", "dateModified": "2017-04-05T19:38:32Z" } }, { "key": "MD5CPAKT", "version": 59, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/MD5CPAKT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/MD5CPAKT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/CBCIUF7D", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "MD5CPAKT", "version": 59, "parentItem": "CBCIUF7D", "itemType": "attachment", "linkMode": "imported_url", "title": "1471-2105-7-208.fm - 1471-2105-7-208.pdf", "accessDate": "2015-11-06T11:54:59Z", "url": "http://www.biomedcentral.com/content/pdf/1471-2105-7-208.pdf", "note": "", "contentType": "application/pdf", "charset": "utf-8", "filename": "1471-2105-7-208.pdf", "md5": "17afcc4c5bf4795dc9875d936debdc6c", "mtime": 1491421077000, "tags": [], "relations": {}, "dateAdded": "2017-04-05T19:37:57Z", "dateModified": "2017-04-05T19:37:57Z" } }, { "key": "CBCIUF7D", "version": 58, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/CBCIUF7D", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/CBCIUF7D", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Peng et al.", "parsedDate": "2006", "numChildren": 1 }, "data": { "key": "CBCIUF7D", "version": 58, "itemType": "journalArticle", "title": "Length-dependent prediction of protein intrinsic disorder", "creators": [ { "creatorType": "author", "firstName": "Kang", "lastName": "Peng" }, { "creatorType": "author", "firstName": "Predrag", "lastName": "Radivojac" }, { "creatorType": "author", "firstName": "Slobodan", "lastName": "Vucetic" }, { "creatorType": "author", "firstName": "A. Keith", "lastName": "Dunker" }, { "creatorType": "author", "firstName": "Zoran", "lastName": "Obradovic" } ], "abstractNote": "", "publicationTitle": "BMC bioinformatics", "publisher": "", "place": "", "date": "2006", "volume": "7", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "208", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.biomedcentral.com/1471-2105/7/208", "accessDate": "2015-11-06T11:55:29Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "6EXCB4HX" ], "relations": {}, "dateAdded": "2017-04-05T19:37:57Z", "dateModified": "2017-04-05T19:37:57Z" } }, { "key": "2MEZVBRG", "version": 58, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/2MEZVBRG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/2MEZVBRG", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/GKC267BG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } } }, "data": { "key": "2MEZVBRG", "version": 58, "parentItem": "GKC267BG", "itemType": "attachment", "linkMode": "imported_url", "title": "ScienceDirect Snapshot", "accessDate": "2016-05-06T16:38:14Z", "url": "http://www.sciencedirect.com/science/article/pii/S0022283605001294", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "S0022283605001294.html", "md5": "a9dc3df38270de19337fd783f6e8b9d0", "mtime": 1491421054000, "tags": [], "relations": {}, "dateAdded": "2017-04-05T19:37:33Z", "dateModified": "2017-04-05T19:37:33Z" } }, { "key": "ZPQWKK4A", "version": 58, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/ZPQWKK4A", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/ZPQWKK4A", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/GKC267BG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "ZPQWKK4A", "version": 58, "parentItem": "GKC267BG", "itemType": "attachment", "linkMode": "imported_url", "title": "ScienceDirect Full Text PDF", "accessDate": "2016-05-06T16:38:14Z", "url": "http://www.sciencedirect.com/science/article/pii/S0022283605001294/pdfft?md5=364b3bdf588d9741d48e6747cb8f4e2e&pid=1-s2.0-S0022283605001294-main.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Dosztányi et al. - 2005 - The Pairwise Energy Content Estimated from Amino A.pdf", "md5": "a4040ba07129bc599a89ef9e0f04251a", "mtime": 1491421054000, "tags": [], "relations": {}, "dateAdded": "2017-04-05T19:37:33Z", "dateModified": "2017-04-05T19:37:33Z" } }, { "key": "GKC267BG", "version": 57, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/GKC267BG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/GKC267BG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Dosztányi et al.", "parsedDate": "2005", "numChildren": 2 }, "data": { "key": "GKC267BG", "version": 57, "itemType": "journalArticle", "title": "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins", "creators": [ { "creatorType": "author", "firstName": "Zsuzsanna", "lastName": "Dosztányi" }, { "creatorType": "author", "firstName": "Veronika", "lastName": "Csizmók" }, { "creatorType": "author", "firstName": "Péter", "lastName": "Tompa" }, { "creatorType": "author", "firstName": "István", "lastName": "Simon" } ], "abstractNote": "The structural stability of a protein requires a large number of interresidue interactions. The energetic contribution of these can be approximated by low-resolution force fields extracted from known structures, based on observed amino acid pairing frequencies. The summation of such energies, however, cannot be carried out for proteins whose structure is not known or for intrinsically unstructured proteins. To overcome these limitations, we present a novel method for estimating the total pairwise interaction energy, based on a quadratic form in the amino acid composition of the protein. This approach is validated by the good correlation of the estimated and actual energies of proteins of known structure and by a clear separation of folded and disordered proteins in the energy space it defines. As the novel algorithm has not been trained on unstructured proteins, it substantiates the concept of protein disorder, i.e. that the inability to form a well-defined 3D structure is an intrinsic property of many proteins and protein domains. This property is encoded in their sequence, because their biased amino acid composition does not allow sufficient stabilizing interactions to form. By limiting the calculation to a predefined sequential neighborhood, the algorithm was turned into a position-specific scoring scheme that characterizes the tendency of a given amino acid to fall into an ordered or disordered region. This application we term IUPred and compare its performance with three generally accepted predictors, PONDR VL3H, DISOPRED2 and GlobPlot on a database of disordered proteins.", "publicationTitle": "Journal of Molecular Biology", "publisher": "", "place": "", "date": "Abril 8, 2005", "volume": "347", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "827-839", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Journal of Molecular Biology", "DOI": "10.1016/j.jmb.2005.01.071", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0022283605001294", "accessDate": "2016-05-06T16:38:14Z", "PMID": "", "PMCID": "", "ISSN": "0022-2836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "foldability", "type": 1 }, { "tag": "interresidue interactions", "type": 1 }, { "tag": "intrinsically unstructured proteins", "type": 1 }, { "tag": "low-resolution force fields", "type": 1 }, { "tag": "prediction of disordered proteins", "type": 1 } ], "collections": [ "6EXCB4HX" ], "relations": {}, "dateAdded": "2017-04-05T19:37:33Z", "dateModified": "2017-04-05T19:37:33Z" } }, { "key": "N2QEXMFI", "version": 57, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/N2QEXMFI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/N2QEXMFI", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/625558/items/AS859IS7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "N2QEXMFI", "version": 57, "parentItem": "AS859IS7", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2015-11-06T11:47:32Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169197/pdf/gkg519.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Linding et al. - 2003 - GlobPlot exploring protein sequences for globular.pdf", "md5": "4057040ea9233df21997e6324446b866", "mtime": 1491421031000, "tags": [], "relations": {}, "dateAdded": "2017-04-05T19:37:11Z", "dateModified": "2017-04-05T19:37:11Z" } }, { "key": "MHQJ4F5R", "version": 56, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/MHQJ4F5R", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/MHQJ4F5R", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Linding et al.", "parsedDate": "2003", "numChildren": 0 }, "data": { "key": "MHQJ4F5R", "version": 56, "itemType": "journalArticle", "title": "Protein Disorder Prediction", "creators": [ { "creatorType": "author", "firstName": "Rune", "lastName": "Linding" }, { "creatorType": "author", "firstName": "Lars Juhl", "lastName": "Jensen" }, { "creatorType": "author", "firstName": "Francesca", "lastName": "Diella" }, { "creatorType": "author", "firstName": "Peer", "lastName": "Bork" }, { "creatorType": "author", "firstName": "Toby J", "lastName": "Gibson" }, { "creatorType": "author", "firstName": "Robert B", "lastName": "Russell" } ], "abstractNote": "", "publicationTitle": "Structure", "publisher": "", "place": "", "date": "11/2003", "volume": "11", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "1453-1459", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.str.2003.10.002", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/S0969212603002351", "accessDate": "2015-11-06T11:45:26Z", "PMID": "", "PMCID": "", "ISSN": "09692126", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "6EXCB4HX" ], "relations": {}, "dateAdded": "2017-04-05T19:37:11Z", "dateModified": "2017-04-05T19:37:11Z" } }, { "key": "AS859IS7", "version": 56, "library": { "type": "group", "id": 625558, "name": "modelagem", "links": { "alternate": { "href": "https://www.zotero.org/groups/modelagem", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/625558/items/AS859IS7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/modelagem/items/AS859IS7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2724767, "username": "dmresende", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/dmresende", "type": "text/html" } } }, "creatorSummary": "Linding et al.", "parsedDate": "2003-07-01", "numChildren": 2 }, "data": { "key": "AS859IS7", "version": 56, "itemType": "journalArticle", "title": "GlobPlot: exploring protein sequences for globularity and disorder", "creators": [ { "creatorType": "author", "firstName": "Rune", "lastName": "Linding" }, { "creatorType": "author", "firstName": "Robert B.", "lastName": "Russell" }, { "creatorType": "author", "firstName": "Victor", "lastName": "Neduva" }, { "creatorType": "author", "firstName": "Toby J.", "lastName": "Gibson" } ], "abstractNote": "A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Non-globular sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http://globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface—GlobPipe—for the advanced user to do whole proteome analysis. 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