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On the general nature of the RNA code.", "creators": [ { "creatorType": "author", "firstName": "M", "lastName": "Nirenberg" }, { "creatorType": "author", "firstName": "P", "lastName": "Leder" }, { "creatorType": "author", "firstName": "M", "lastName": "Bernfield" }, { "creatorType": "author", "firstName": "R", "lastName": "Brimacombe" }, { "creatorType": "author", "firstName": "J", "lastName": "Trupin" }, { "creatorType": "author", "firstName": "F", "lastName": "Rottman" }, { "creatorType": "author", "firstName": "C", "lastName": "O'Neal" } ], "abstractNote": "", "publicationTitle": "Proceedings of the National Academy of Sciences of the United States of America", "publisher": "", "place": "", "date": "1965-5", "volume": "53", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "1161-1168", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc Natl Acad Sci U S A", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0027-8424", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 5330357\nPMCID: 301388", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2011-10-27T19:44:00Z", "dateModified": "2011-10-27T19:44:00Z" } }, { "key": "MXMB3JRU", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/MXMB3JRU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/MXMB3JRU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/20291/items/NV63WU54", "type": "application/json" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } } }, "data": { "key": "MXMB3JRU", "version": 1, "parentItem": "NV63WU54", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2011-10-27T19:44:00Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC301388/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2011-10-27T19:44:00Z", "dateModified": "2011-10-27T19:44:00Z" } }, { "key": "76U943Z8", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/76U943Z8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/76U943Z8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "McCarty and Avery", "parsedDate": "1946-01-31", "numChildren": 1 }, "data": { "key": "76U943Z8", "version": 1, "itemType": "journalArticle", "title": "STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES", "creators": [ { "creatorType": "author", "firstName": "Maclyn", "lastName": "McCarty" }, { "creatorType": "author", "firstName": "Oswald T.", "lastName": "Avery" } ], "abstractNote": "1. An improved method is outlined for the isolation and purification of the pneumococcal transforming substance. This method makes use of the fact that citrate inhibits the destructive action of the enzyme, desoxyribonuclease, which is released together with the active material during lysis of the living bacterial cells. A fivefold greater yield of purified transforming agent is obtained by the present method than by the procedure previousiy described. 2. The specific transforming substance has been isolated from pneumococci of types II and VI, in addition to Type III. In each instance the biologically active material has been found to consist of desoxyribonucleic acid.", "publicationTitle": "The Journal of Experimental Medicine", "publisher": "", "place": "", "date": "1946-1-31", "volume": "83", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "97-104", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Exp Med", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0022-1007", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 19871521\nPMCID: 2135577", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2011-10-27T19:24:53Z", "dateModified": "2011-10-27T19:24:53Z" } }, { "key": "C7DVNG8H", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/C7DVNG8H", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/C7DVNG8H", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/20291/items/76U943Z8", "type": "application/json" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } } }, "data": { "key": "C7DVNG8H", "version": 1, "parentItem": "76U943Z8", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2011-10-27T19:24:53Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2135577/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2011-10-27T19:24:53Z", "dateModified": "2011-10-27T19:24:53Z" } }, { "key": "QVWI4B75", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/QVWI4B75", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/QVWI4B75", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "WATSON and CRICK", "parsedDate": "1953-04-25", "numChildren": 0 }, "data": { "key": "QVWI4B75", "version": 1, "itemType": "journalArticle", "title": "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid", "creators": [ { "creatorType": "author", "firstName": "J D", "lastName": "WATSON" }, { "creatorType": "author", "firstName": "F H", "lastName": "CRICK" } ], "abstractNote": "", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "Apr 25, 1953", "volume": "171", "issue": "4356", "section": "", "partNumber": "", "partTitle": "", "pages": "737-738", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/13054692", "accessDate": "2011-10-27T19:21:51Z", "PMID": "", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 13054692", "tags": [ { "tag": "Nucleic Acids", "type": 1 } ], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2011-10-27T19:21:51Z", "dateModified": "2011-10-27T19:21:51Z" } }, { "key": "GGVRFQCU", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/GGVRFQCU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/GGVRFQCU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Herrmann et al.", "parsedDate": "2002-05-24", "numChildren": 0 }, "data": { "key": "GGVRFQCU", "version": 1, "itemType": "journalArticle", "title": "Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA", "creators": [ { "creatorType": "author", "firstName": "Torsten", "lastName": "Herrmann" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Güntert" }, { "creatorType": "author", "firstName": "Kurt", "lastName": "Wüthrich" } ], "abstractNote": "Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated assignment of the NOESY spectra. CANDID uses an iterative approach with multiple cycles of NOE cross-peak assignment and protein structure calculation using the fast DYANA torsion angle dynamics algorithm, so that the result from each CANDID cycle consists of exhaustive, possibly ambiguous NOE cross-peak assignments in all available spectra and a three-dimensional protein structure represented by a bundle of conformers. The input for the first CANDID cycle consists of the amino acid sequence, the chemical shift list from the sequence-specific resonance assignment, and listings of the cross-peak positions and volumes in one or several two, three or four-dimensional NOESY spectra. The input for the second and subsequent CANDID cycles contains the three-dimensional protein structure from the previous cycle, in addition to the complete input used for the first cycle. CANDID includes two new elements that make it robust with respect to the presence of artifacts in the input data, i.e. network-anchoring and constraint-combination, which have a key role in de novo protein structure determinations for the successful generation of the correct polypeptide fold by the first CANDID cycle. Network-anchoring makes use of the fact that any network of correct NOE cross-peak assignments forms a self-consistent set; the initial, chemical shift-based assignments for each individual NOE cross-peak are therefore weighted by the extent to which they can be embedded into the network formed by all other NOE cross-peak assignments. Constraint-combination reduces the deleterious impact of artifact NOE upper distance constraints in the input for a protein structure calculation by combining the assignments for two or several peaks into a single upper limit distance constraint, which lowers the probability that the presence of an artifact peak will influence the outcome of the structure calculation. CANDID test calculations were performed with NMR data sets of four proteins for which high-quality structures had previously been solved by interactive protocols, and they yielded comparable results to these reference structure determinations with regard to both the residual constraint violations, and the precision and accuracy of the atomic coordinates. The CANDID approach has further been validated by de novo NMR structure determinations of four additional proteins. The experience gained in these calculations shows that once nearly complete sequence-specific resonance assignments are available, the automated CANDID approach results in greatly enhanced efficiency of the NOESY spectral analysis. The fact that the correct fold is obtained in cycle 1 of a de novo structure calculation is the single most important advance achieved with CANDID, when compared with previously proposed automated NOESY assignment methods that do not use network-anchoring and constraint-combination.", "publicationTitle": "Journal of Molecular Biology", "publisher": "", "place": "", "date": "May 24, 2002", "volume": "319", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "209-227", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Mol. Biol", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/12051947", "accessDate": "2011-07-05T21:57:57Z", "PMID": "", "PMCID": "", "ISSN": "0022-2836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 12051947", "tags": [ { "tag": "Algorithms", "type": 1 }, { "tag": "Animals", "type": 1 }, { "tag": "Bacterial Proteins", "type": 1 }, { "tag": "Cattle", "type": 1 }, { "tag": "Killer Factors, Yeast", "type": 1 }, { "tag": "Models, Molecular", "type": 1 }, { "tag": "Molecular Chaperones", "type": 1 }, { "tag": "Mycotoxins", "type": 1 }, { "tag": "Nuclear Magnetic Resonance, Biomolecular", "type": 1 }, { "tag": "Peptide Fragments", "type": 1 }, { "tag": "Plant Proteins", "type": 1 }, { "tag": "Prions", "type": 1 }, { "tag": "Protein Conformation", "type": 1 }, { "tag": "Proteins", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Trans-Activators", "type": 1 } ], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2011-07-05T21:57:57Z", "dateModified": "2011-07-05T21:57:57Z" } }, { "key": "DMUEQ85M", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/DMUEQ85M", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/DMUEQ85M", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Saccenti and Rosato", "parsedDate": "2008-04", "numChildren": 0 }, "data": { "key": "DMUEQ85M", "version": 1, "itemType": "journalArticle", "title": "The war of tools: how can NMR spectroscopists detect errors in their structures?", "creators": [ { "creatorType": "author", "firstName": "Edoardo", "lastName": "Saccenti" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Rosato" } ], "abstractNote": "Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to which these tools could be applied to detect flaws in NMR structures. In particular, we investigated the variation in the scores assigned by these programs as a function of the deviation of the structures induced by errors in assignments or in the upper distance limits used. These perturbations did not distort radically the protein fold, but resulted in backbone RMS deviations up to 3 A, which is in line with errors highlighted in the available literature. We found that it is quite difficult to discriminate the structures perturbed because of misassignments from the original ones, also because the spread in score over the conformers of the original bundle is relatively large. varphi-psi distributions and normality scores related to the backbone conformation and to the distribution of side-chain dihedral angles are the most sensitive indicators of flaws.", "publicationTitle": "Journal of Biomolecular NMR", "publisher": "", "place": "", "date": "Apr 2008", "volume": "40", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "251-261", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Biomol. NMR", "DOI": "10.1007/s10858-008-9228-4", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18320330", "accessDate": "2011-07-05T20:11:47Z", "PMID": "", "PMCID": "", "ISSN": "0925-2738", "archive": "", "archiveLocation": "", "shortTitle": "The war of tools", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 18320330", "tags": [ { "tag": "Calcium-Binding Protein, Vitamin D-Dependent", "type": 1 }, { "tag": "Magnetic Resonance Spectroscopy", "type": 1 }, { "tag": "Models, Molecular", "type": 1 }, { "tag": "Protein Folding", "type": 1 }, { "tag": "Protein Structure, Secondary", "type": 1 }, { "tag": "Proteins", "type": 1 }, { "tag": "Reproducibility of Results", "type": 1 }, { "tag": "Software", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2011-07-05T20:11:47Z", "dateModified": "2011-07-05T20:11:47Z" } }, { "key": "22NZDWWZ", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/22NZDWWZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/22NZDWWZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Raman et al.", "parsedDate": "2010-01-13", "numChildren": 0 }, "data": { "key": "22NZDWWZ", "version": 1, "itemType": "journalArticle", "title": "Accurate automated protein NMR structure determination using unassigned NOESY data", "creators": [ { "creatorType": "author", "firstName": "Srivatsan", "lastName": "Raman" }, { "creatorType": "author", "firstName": "Yuanpeng J", "lastName": "Huang" }, { "creatorType": "author", "firstName": "Binchen", "lastName": "Mao" }, { "creatorType": "author", "firstName": "Paolo", "lastName": "Rossi" }, { "creatorType": "author", "firstName": "James M", "lastName": "Aramini" }, { "creatorType": "author", "firstName": "Gaohua", "lastName": "Liu" }, { "creatorType": "author", "firstName": "Gaetano T", "lastName": "Montelione" }, { "creatorType": "author", "firstName": "David", "lastName": "Baker" } ], "abstractNote": "Conventional NMR structure determination requires nearly complete assignment of the cross peaks of a refined NOESY peak list. Depending on the size of the protein and quality of the spectral data, this can be a time-consuming manual process requiring several rounds of peak list refinement and structure determination. Programs such as Aria, CYANA, and AutoStructure can generate models using unassigned NOESY data but are very sensitive to the quality of the input peak lists and can converge to inaccurate structures if the signal-to-noise of the peak lists is low. Here, we show that models with high accuracy and reliability can be produced by combining the strengths of the high-resolution structure prediction program Rosetta with global measures of the agreement between structure models and experimental data. A first round of models generated using CS-Rosetta (Rosetta supplemented with backbone chemical shift information) are filtered on the basis of their goodness-of-fit with unassigned NOESY peak lists using the DP-score, and the best fitting models are subjected to high resolution refinement with the Rosetta rebuild-and-refine protocol. This hybrid approach uses both local backbone chemical shift and the unassigned NOESY data to direct Rosetta trajectories toward the native structure and produces more accurate models than AutoStructure/CYANA or CS-Rosetta alone, particularly when using raw unedited NOESY peak lists. We also show that when accurate manually refined NOESY peak lists are available, Rosetta refinement can consistently increase the accuracy of models generated using CYANA and AutoStructure.", "publicationTitle": "Journal of the American Chemical Society", "publisher": "", "place": "", "date": "Jan 13, 2010", "volume": "132", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "202-207", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Am. Chem. Soc", "DOI": "10.1021/ja905934c", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20000319", "accessDate": "2011-07-05T20:07:30Z", "PMID": "", "PMCID": "", "ISSN": "1520-5126", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 20000319", "tags": [ { "tag": "Automation", "type": 1 }, { "tag": "Crystallography, X-Ray", "type": 1 }, { "tag": "Models, Molecular", "type": 1 }, { "tag": "Nuclear Magnetic Resonance, Biomolecular", "type": 1 }, { "tag": "Protein Conformation", "type": 1 }, { "tag": "Proteins", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2011-07-05T20:07:30Z", "dateModified": "2011-07-05T20:07:30Z" } }, { "key": "BR5KIXMT", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/BR5KIXMT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/BR5KIXMT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "BR5KIXMT", "version": 1, "itemType": "document", "title": "RCSB PDB Statistics", "creators": [], "abstractNote": "", "type": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://www.pdb.org/pdb/static.do?p=general_information/pdb_statistics/index.html", "accessDate": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-07-04T17:17:00Z", "dateModified": "2011-07-04T17:17:19Z" } }, { "key": "NUBX9935", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/NUBX9935", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/NUBX9935", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "NUBX9935", "version": 1, "itemType": "journalArticle", "title": "", "creators": [], "abstractNote": "", "publicationTitle": "", "publisher": "", "place": "", "date": "", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-07-04T17:16:52Z", "dateModified": "2011-07-04T17:16:52Z" } }, { "key": "XPWUVIBI", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/XPWUVIBI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/XPWUVIBI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Mobli et al.", "parsedDate": "2007-10", "numChildren": 0 }, "data": { "key": "XPWUVIBI", "version": 1, "itemType": "journalArticle", "title": "Automatic maximum entropy spectral reconstruction in NMR", "creators": [ { "creatorType": "author", "firstName": "Mehdi", "lastName": "Mobli" }, { "creatorType": "author", "firstName": "Mark W", "lastName": "Maciejewski" }, { "creatorType": "author", "firstName": "Michael R", "lastName": "Gryk" }, { "creatorType": "author", "firstName": "Jeffrey C", "lastName": "Hoch" } ], "abstractNote": "Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system.", "publicationTitle": "Journal of Biomolecular NMR", "publisher": "", "place": "", "date": "Oct 2007", "volume": "39", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "133-139", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Biomol. NMR", "DOI": "10.1007/s10858-007-9180-8", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/17701276", "accessDate": "2010-07-27T20:21:49Z", "PMID": "", "PMCID": "", "ISSN": "0925-2738", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 17701276", "tags": [ { "tag": "Actin Depolymerizing Factors", "type": 1 }, { "tag": "Entropy", "type": 1 }, { "tag": "Internet", "type": 1 }, { "tag": "Nitrogen Isotopes", "type": 1 }, { "tag": "Nuclear Magnetic Resonance, Biomolecular", "type": 1 }, { "tag": "Protons", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Software Design", "type": 1 }, { "tag": "User-Computer Interface", "type": 1 } ], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-07-27T20:21:49Z", "dateModified": "2010-07-27T20:21:49Z" } }, { "key": "EFXT7Z9G", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/EFXT7Z9G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/EFXT7Z9G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "EFXT7Z9G", "version": 1, "itemType": "blogPost", "title": "JEOL Ltd.", "creators": [], "abstractNote": "", "blogTitle": "", "websiteType": "", "date": "", "DOI": "", "citationKey": "", "url": "http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/", "accessDate": "", "ISSN": "", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-07-27T20:19:13Z", "dateModified": "2010-07-27T20:20:09Z" } }, { "key": "JFAUVJJH", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/JFAUVJJH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/JFAUVJJH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Bruker BioSpin and Bruker BioSpin", "numChildren": 0 }, "data": { "key": "JFAUVJJH", "version": 1, "itemType": "webpage", "title": "Bruker BioSpin - Analytical Instruments based on NMR, EPR and MRI by Bruker | Bruker BioSpin", "creators": [ { "creatorType": "author", "firstName": "", "lastName": "Bruker BioSpin" }, { "creatorType": "author", "firstName": "", "lastName": "Bruker BioSpin" } ], "abstractNote": "", "websiteTitle": "", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://www.bruker-biospin.com/", "accessDate": "2010-07-27T20:18:27Z", "shortTitle": "", "language": "", "rights": "", "extra": "Bruker BioSpin is the market leader in NMR spectroscopy, EPR, and pre-clinical MRI. BioSpin offers the world's most comprehensive biotechnology range of life science.", "tags": [ { "tag": "NMR,MRI,MRT,EPR,ESR,Spectroscopy,Bruker,Metabolomics,Proteomics,Imaging,Biotechnology,Metabonomics,Life Science,Magnetic Resonance,Analytical Chemistry,Molecular Imaging,Clinical Research,Molecular Spectroscopy,Analytical Instruments,Superconducting Magne", "type": 1 } ], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-07-27T20:18:27Z", "dateModified": "2010-07-27T20:18:27Z" } }, { "key": "B2HRKNEE", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/B2HRKNEE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/B2HRKNEE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "B2HRKNEE", "version": 1, "itemType": "blogPost", "title": "Varian/Agilent NMR", "creators": [], "abstractNote": "", "blogTitle": "", "websiteType": "", "date": "", "DOI": "", "citationKey": "", "url": "http://www.varianinc.com/cgi-bin/nav?/products/nmr/", "accessDate": "", "ISSN": "", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-07-27T20:17:21Z", "dateModified": "2010-07-27T20:18:11Z" } }, { "key": "5FFINDE7", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/5FFINDE7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/5FFINDE7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/20291/items/A884QIVG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "5FFINDE7", "version": 1, "parentItem": "A884QIVG", "itemType": "note", "note": "CiteSeerX - Scientific Literature Digital Library and Search\nEngine [http://citeseerx.ist.psu.edu/oai2] (United States)\nER", "tags": [], "relations": {}, "dateAdded": "2010-07-27T19:05:43Z", "dateModified": "2010-07-27T19:05:43Z" } }, { "key": "A884QIVG", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/A884QIVG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/A884QIVG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Ingo Wassink et al.", "parsedDate": "2010-04-06", "numChildren": 1 }, "data": { "key": "A884QIVG", "version": 1, "itemType": "document", "title": "2009 Congress on Services- I Analysing scientific workflows: why workflows not only connect web services", "creators": [ { "creatorType": "author", "firstName": "", "lastName": "Ingo Wassink" }, { "creatorType": "author", "firstName": "", "lastName": "Paul E. Van Der Vet" }, { "creatorType": "author", "firstName": "", "lastName": "Katy Wolstencroft" }, { "creatorType": "author", "firstName": "", "lastName": "Pieter B. T. Neerincx" }, { "creatorType": "author", "firstName": "", "lastName": "Marco Roos" }, { "creatorType": "author", "firstName": "", "lastName": "Han Rauwerda" }, { "creatorType": "author", "firstName": "", "lastName": "Timo M. Breit" }, { "creatorType": "author", "firstName": "", "lastName": "The Netherl" }, { "creatorType": "author", "firstName": "", "lastName": "S Bioinformatics Centre" } ], "abstractNote": "Abstract—Life science workflow systems are developed to\nhelp life scientists to conveniently connect various\nprograms and web services. In practice however, much time is\nspent on data conversion, because web services provided by\ndifferent organisations use different data formats. We have\nanalysed all the Taverna workflows available at the\nmyExperiment web site on December 11, 2008. Our analysis of\nthe tasks in these workflows shows several noticeable\naspects: their number ranges from 1 to 70 tasks per\nworkflow; 18 % of the workflows consist of a single task. Of\nthe tasks used are 22 % web services; local services, i.e.\ntasks executed by the workflow system itself, are very\npopular and cover 57 % of tasks; tasks implemented by the\nworkflow designer, scripting tasks, are is also used often\n(14%). Our analysis shows that over 30 % of tasks are\nrelated to data conversion. Keywords-Scientific workflow;\ndata conversion; web services; scripting; sub-workflow I.", "type": "", "date": "April 06, 2010", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.159.9202", "accessDate": "2010-07-27T19:05:42Z", "archive": "", "archiveLocation": "", "shortTitle": "2009 Congress on Services- I Analysing scientific workflows", "language": "", "libraryCatalog": "ScientificCommons", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-07-27T19:05:42Z", "dateModified": "2010-07-27T19:05:42Z" } }, { "key": "R4T74MQF", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/R4T74MQF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/R4T74MQF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Linge et al.", "parsedDate": "1999-10-01", "numChildren": 0 }, "data": { "key": "R4T74MQF", "version": 1, "itemType": "journalArticle", "title": "StarDOM: From STAR format to XML", "creators": [ { "creatorType": "author", "firstName": "Jens P.", "lastName": "Linge" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Nilges" }, { "creatorType": "author", "firstName": "Lutz", "lastName": "Ehrlich" } ], "abstractNote": "StarDOM is a software package for the representation of STAR files as document object models and the conversion of STAR files into XML. This allows interactive navigation by using the Document Object Model representation of the data as well as easy access by XML query languages. As an example application, the entire BioMagResBank has been transformed into XML format. Using an XML query language, statistical queries on the collected NMR data sets can be constructed with very little effort. The BioMagResBank/XML data and the software can be obtained at http://www.nmr.embl-heidelberg.de/nmr/StarDOM/", "publicationTitle": "Journal of Biomolecular NMR", "publisher": "", "place": "", "date": "October 01, 1999", "volume": "15", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "169-172", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1023/A:1008347330165", "citationKey": "", "url": "http://dx.doi.org/10.1023/A:1008347330165", "accessDate": "2010-06-16T20:35:07Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "StarDOM", "language": "", "libraryCatalog": "SpringerLink", "callNumber": "0005", "rights": "", "extra": "", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-06-16T20:35:07Z", "dateModified": "2010-06-28T16:38:20Z" } }, { "key": "ZTVSQXIA", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/ZTVSQXIA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/ZTVSQXIA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Wishart", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "ZTVSQXIA", "version": 1, "itemType": "journalArticle", "title": "CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.", "creators": [ { "creatorType": "author", "firstName": "D. S.", "lastName": "Wishart" } ], "abstractNote": "", "publicationTitle": "Nucleic acids research", "publisher": "", "place": "", "date": "2008", "volume": "36", "issue": "Web Server issue", "section": "", "partNumber": "", "partTitle": "", "pages": "W496-502", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.scopus.com/inward/record.url?eid=2-s2.0-48449095850&partnerID=40&md5=8547d8263500b6d8638e9476a2f5dc9a", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0021", "rights": "", "extra": "cited By (since 1996) 20", "tags": [], "collections": [ "3BTD6PG8" ], "relations": {}, "dateAdded": "2010-06-15T19:50:16Z", "dateModified": "2010-06-28T16:17:58Z" } }, { "key": "ZT7KVBSK", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/ZT7KVBSK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/ZT7KVBSK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Heinemann", "parsedDate": "2001", "numChildren": 0 }, "data": { "key": "ZT7KVBSK", "version": 1, "itemType": "journalArticle", "title": "High-throughput three-dimensional protein structure determination", "creators": [ { "creatorType": "author", "firstName": "U.", "lastName": "Heinemann" } ], "abstractNote": "", "publicationTitle": "Current Opinion in Biotechnology", "publisher": "", "place": "", "date": "2001", "volume": "12", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "348-354", 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"2010-06-28T16:17:55Z" } }, { "key": "WKP72WTZ", "version": 1, "library": { "type": "group", "id": 20291, "name": "Protein NMR", "links": { "alternate": { "href": "https://www.zotero.org/groups/protein_nmr", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/20291/items/WKP72WTZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/protein_nmr/items/WKP72WTZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 987, "username": "glob157", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/glob157", "type": "text/html" } } }, "creatorSummary": "Ramelot et al.", "parsedDate": "2009-04", "numChildren": 0 }, "data": { "key": "WKP72WTZ", "version": 1, "itemType": "journalArticle", "title": "Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study", "creators": [ { "creatorType": "author", "firstName": "Theresa A", "lastName": "Ramelot" }, { "creatorType": "author", "firstName": "Srivatsan", "lastName": "Raman" }, { "creatorType": "author", "firstName": "Alexandre P", "lastName": "Kuzin" }, { "creatorType": "author", "firstName": "Rong", "lastName": "Xiao" }, { "creatorType": "author", "firstName": "Li-Chung", "lastName": "Ma" }, { "creatorType": "author", "firstName": "Thomas B", "lastName": "Acton" }, { "creatorType": "author", "firstName": "John F", "lastName": "Hunt" }, { "creatorType": "author", "firstName": "Gaetano T", "lastName": "Montelione" }, { "creatorType": "author", "firstName": "David", "lastName": "Baker" }, { "creatorType": "author", "firstName": "Michael A", "lastName": "Kennedy" } ], "abstractNote": "The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffraction data using MOLREP and Phaser. This method has recently been shown to be generally applicable with improved MR performance demonstrated for eight NMR structures refined using Rosetta (Qian et al., Nature 2007;450:259-264). Additionally, NMR structures of HSPC034 calculated by standard methods that include NMR restraints have improvements in the RMSD to the crystal structure and MR performance in the order DYANA, CYANA, XPLOR-NIH, and CNS with explicit water refinement (CNSw). 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