{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T14:51:52Z","timestamp":1787064712181,"version":"build-2736575974"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1395,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: ADAPT-nuclear magnetic resonance (ADAPT-NMR) offers an automated approach to the concurrent acquisition and processing of protein NMR data with the goal of complete backbone and side chain assignments. What the approach lacks is a useful graphical interface for reviewing results and for searching for missing peaks that may have prevented assignments or led to incorrect assignments. Because most of the data ADAPT-NMR collects are 2D tilted planes used to find peaks in 3D spectra, it would be helpful to have a tool that reconstructs the 3D spectra. The software package reported here, ADAPT-NMR Enhancer, supports the visualization of both 2D tilted planes and reconstructed 3D peaks on each tilted plane. ADAPT-NMR Enhancer can be used interactively with ADAPT-NMR to automatically assign selected peaks, or it can be used to produce PINE-SPARKY-like graphical dialogs that support atom-by-atom and peak-by-peak assignment strategies. Results can be exported in various formats, including XEASY proton file (.prot), PINE pre-assignment file (.str), PINE probabilistic output file, SPARKY peak list file (.list) and TALOS+ input file (.tab). As an example, we show how ADAPT-NMR Enhancer was used to extend the automated data collection and assignment results for the protein Aedes aegypti sterol carrier protein 2.<\/jats:p>\n                  <jats:p>Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http:\/\/pine.nmrfam.wisc.edu\/adapt-nmr-enhancer.<\/jats:p>\n                  <jats:p>Contact: \u00a0whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts692","type":"journal-article","created":{"date-parts":[[2012,12,8]],"date-time":"2012-12-08T22:09:37Z","timestamp":1355004577000},"page":"515-517","source":"Crossref","is-referenced-by-count":8,"title":["ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy"],"prefix":"10.1093","volume":"29","author":[{"given":"Woonghee","family":"Lee","sequence":"first","affiliation":[{"name":"1 National Magnetics Resonance Facility at Madison and 2Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA"},{"name":"1 National Magnetics Resonance Facility at Madison and 2Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arash","family":"Bahrami","sequence":"additional","affiliation":[{"name":"1 National Magnetics Resonance Facility at Madison and 2Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John L.","family":"Markley","sequence":"additional","affiliation":[{"name":"1 National Magnetics Resonance Facility at Madison and 2Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA"},{"name":"1 National Magnetics Resonance Facility at Madison and 2Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,12,7]]},"reference":[{"key":"2023012810233755300_bts692-B1","doi-asserted-by":"crossref","first-page":"e1000307","DOI":"10.1371\/journal.pcbi.1000307","article-title":"Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy","volume":"5","author":"Bahrami","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012810233755300_bts692-B2","doi-asserted-by":"crossref","first-page":"e33173","DOI":"10.1371\/journal.pone.0033173","article-title":"Integrated protein NMR data collection and assignment by the ADAPT-NMR approach","volume":"7","author":"Bahrami","year":"2012","journal-title":"PLoS One"},{"key":"2023012810233755300_bts692-B3","doi-asserted-by":"crossref","first-page":"12528","DOI":"10.1021\/ja052120i","article-title":"High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection","volume":"127","author":"Eghbalnia","year":"2005","journal-title":"J. Am. Chem. Soc."},{"key":"2023012810233755300_bts692-B5","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/S0163-7827(01)00015-7","article-title":"Gene structure, intracellular location, and functional roles of sterol carrier protein-2","volume":"40","author":"Gallegos","year":"2001","journal-title":"Prog. Lipid Res."},{"key":"2023012810233755300_bts692-B4","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1093\/bioinformatics\/btp345","article-title":"PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy","volume":"25","author":"Lee","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810233755300_bts692-B6","doi-asserted-by":"crossref","first-page":"17046","DOI":"10.1074\/jbc.M110.101154","article-title":"Differences in the structure and dynamics of the apo- and palmitate-ligated forms of Aedes aegypti sterol carrier protein 2 (AeSCP-2)","volume":"285","author":"Singarapu","year":"2010","journal-title":"J. Biol. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/4\/515\/48894584\/bioinformatics_29_4_515.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/4\/515\/48894584\/bioinformatics_29_4_515.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T06:52:04Z","timestamp":1674888724000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/4\/515\/197702"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12,7]]},"references-count":6,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2013,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts692","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,2,15]]},"published":{"date-parts":[[2012,12,7]]}}}