{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T14:39:17Z","timestamp":1777473557892,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The inferential structure determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need to be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.bioc.cam.ac.uk\/isd<\/jats:p>\n               <jats:p>Contact: \u00a0wolfgang.rieping@bioc.cam.ac.uk, michael.habeck@tuebingen.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn062","type":"journal-article","created":{"date-parts":[[2008,3,1]],"date-time":"2008-03-01T01:13:23Z","timestamp":1204334003000},"page":"1104-1105","source":"Crossref","is-referenced-by-count":31,"title":["ISD: a software package for Bayesian NMR structure calculation"],"prefix":"10.1093","volume":"24","author":[{"given":"Wolfgang","family":"Rieping","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK, 2Unit\u00e9 de Bioinformatique Structurale, Institut Pasteur, Centre National de la Recherche URA 2185, 25-28, Rue du Dr Roux, 75724 Paris Cedex 15, France and 3Max Planck Institute for Developmental Biology, Spemannstrasse 35 and Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Nilges","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK, 2Unit\u00e9 de Bioinformatique Structurale, Institut Pasteur, Centre National de la Recherche URA 2185, 25-28, Rue du Dr Roux, 75724 Paris Cedex 15, France and 3Max Planck Institute for Developmental Biology, Spemannstrasse 35 and Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Habeck","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK, 2Unit\u00e9 de Bioinformatique Structurale, Institut Pasteur, Centre National de la Recherche URA 2185, 25-28, Rue du Dr Roux, 75724 Paris Cedex 15, France and 3Max Planck Institute for Developmental Biology, Spemannstrasse 35 and Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,28]]},"reference":[{"key":"2023020210002232500_B1","first-page":"11678","article-title":"A framework for scientific data modeling and automated software development","volume":"2","author":"Fogh","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020210002232500_B2","doi-asserted-by":"crossref","first-page":"018105","DOI":"10.1103\/PhysRevLett.94.018105","article-title":"Replica-exchange Monte Carlo scheme for Bayesian data analysis","volume":"94","author":"Habeck","year":"2005","journal-title":"Phys. Rev. Lett."},{"key":"2023020210002232500_B3","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1073\/pnas.0506412103","article-title":"Weighting of experimental evidence in macromolecular structure determination","volume":"103","author":"Habeck","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020210002232500_B4","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s10858-007-9215-1","article-title":"A unifying probabilistic framework for analyzing residual dipolar couplings","volume":"40","author":"Habeck","year":"2008","journal-title":"J. Biomol. NMR"},{"key":"2023020210002232500_B5","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1006\/jmbi.1997.1044","article-title":"Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from spectrin","volume":"269","author":"Nilges","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023020210002232500_B6","article-title":"Quality Criteria for Protein NMR Structures","volume-title":"PhD thesis","author":"Rieping","year":"2005"},{"key":"2023020210002232500_B7","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1126\/science.1110428","article-title":"Inferential structure determination","volume":"309","author":"Rieping","year":"2005","journal-title":"Science"},{"key":"2023020210002232500_B8","doi-asserted-by":"crossref","first-page":"16026","DOI":"10.1021\/ja055092c","article-title":"Modeling errors in NOE data with a lognormal distribution improves the quality of NMR structures","volume":"27","author":"Rieping","year":"2005","journal-title":"J. Am. Chem. Soc."},{"key":"2023020210002232500_B9","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/bioinformatics\/btl589","article-title":"ARIA2: automated NOE assignment and data integration in NMR structure calculation","volume":"23","author":"Rieping","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020210002232500_B10","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1002\/prot.20449","article-title":"The CCPN data model for NMR spectroscopy: development of a software pipeline","volume":"59","author":"Vranken","year":"2005","journal-title":"Proteins"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/8\/1104\/49046049\/bioinformatics_24_8_1104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/8\/1104\/49046049\/bioinformatics_24_8_1104.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:18:10Z","timestamp":1675336690000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/8\/1104\/212671"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,2,28]]},"references-count":10,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2008,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn062","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,4,15]]},"published":{"date-parts":[[2008,2,28]]}}}