{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T20:03:23Z","timestamp":1760731403814,"version":"3.37.3"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"S9","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T00:00:00Z","timestamp":1606953600000},"content-version":"vor","delay-in-days":2,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P20 RR-016461"],"award-info":[{"award-number":["P20 RR-016461"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as \u00b14\u2009Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0\u2009\u00c5 with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4\u2009\u00c5 of the X-ray structure) using only N-H RDCs from one alignment medium.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-020-3522-x","type":"journal-article","created":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T10:03:49Z","timestamp":1606989829000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0320-6894","authenticated-orcid":false,"given":"Casey","family":"Cole","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caleb","family":"Parks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julian","family":"Rachele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Homayoun","family":"Valafar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,12,3]]},"reference":[{"key":"3522_CR1","doi-asserted-by":"publisher","unstructured":"Rodriguez N, Vinal D, Rodriguez-Cobos J, De Castro J, Dominguez G. Genomic profiling in oncology clinical practice. Clin Transl Oncol. 2020. https:\/\/doi.org\/10.1007\/s12094-020-02296-9.","DOI":"10.1007\/s12094-020-02296-9"},{"key":"3522_CR2","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/j.critrevonc.2018.11.008","volume":"133","author":"S Morganti","year":"2019","unstructured":"Morganti S, et al. Complexity of genome sequencing and reporting: next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol. Jan 2019;133:171\u201382. https:\/\/doi.org\/10.1016\/j.critrevonc.2018.11.008.","journal-title":"Crit Rev Oncol Hematol"},{"key":"3522_CR3","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1007\/978-3-030-24100-1_2","volume":"1168","author":"S Morganti","year":"2019","unstructured":"Morganti S, Tarantino P, Ferraro E, D'Amico P, Duso BA, Curigliano G. Next generation sequencing (NGS): a revolutionary Technology in Pharmacogenomics and Personalized Medicine in Cancer. Adv Exp Med Biol. 2019;1168:9\u201330. https:\/\/doi.org\/10.1007\/978-3-030-24100-1_2.","journal-title":"Adv Exp Med Biol"},{"key":"3522_CR4","doi-asserted-by":"publisher","first-page":"308","DOI":"10.3390\/ijms18020308","volume":"18","author":"R Kamps","year":"2017","unstructured":"Kamps R, et al. Next-generation sequencing in oncology: genetic diagnosis, risk prediction and Cancer classification. Int J Mol Sci. 2017;18:308. https:\/\/doi.org\/10.3390\/ijms18020308.","journal-title":"Int J Mol Sci"},{"issue":"2","key":"3522_CR5","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1093\/bib\/bbw114","volume":"19","author":"C Manzoni","year":"2018","unstructured":"Manzoni C, et al. Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. Brief Bioinform. 2018;19(2):286\u2013302. https:\/\/doi.org\/10.1093\/bib\/bbw114.","journal-title":"Brief Bioinform"},{"issue":"4","key":"3522_CR6","doi-asserted-by":"publisher","first-page":"167","DOI":"10.2144\/btn-2019-0030","volume":"66","author":"J Martin","year":"2019","unstructured":"Martin J, Sawyer A. Elucidating the structure of membrane proteins. (in English) Biotechniques. Apr 2019;66(4):167\u201370. https:\/\/doi.org\/10.2144\/btn-2019-0030.","journal-title":"(in English) Biotechniques"},{"issue":"1","key":"3522_CR7","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1002\/pro.3730","volume":"29","author":"DS Goodsell","year":"2020","unstructured":"Goodsell DS, et al. RCSB protein data Bank: enabling biomedical research and drug discovery. Protein Sci. 2020;29(1):52\u201365. https:\/\/doi.org\/10.1002\/pro.3730.","journal-title":"Protein Sci"},{"issue":"6","key":"3522_CR8","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1139\/bcb-2015-0143","volume":"94","author":"A Pandey","year":"2016","unstructured":"Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol. 2016;94(6):507\u201327. https:\/\/doi.org\/10.1139\/bcb-2015-0143.","journal-title":"Biochem Cell Biol"},{"issue":"3","key":"3522_CR9","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1042\/BST20160049","volume":"44","author":"D Hardy","year":"2016","unstructured":"Hardy D, Bill RM, Jawhari A, Rothnie AJ. Overcoming bottlenecks in the membrane protein structural biology pipeline. Biochem Soc Trans. 2016;44(3):838\u201344. https:\/\/doi.org\/10.1042\/BST20160049.","journal-title":"Biochem Soc Trans"},{"key":"3522_CR10","first-page":"179-PHYS","volume":"214","author":"SJ Opella","year":"1997","unstructured":"Opella SJ. Structure determination of membrane proteins by NMR spectroscopy. Abstr Pap Am Chem Soc. 1997;214:179-PHYS.","journal-title":"Abstr Pap Am Chem Soc"},{"key":"3522_CR11","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.jmr.2010.07.016","volume":"207","author":"P Shealy","year":"2010","unstructured":"Shealy P, Simin M, Park SH, Opella SJ, Valafar H. Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein. J Magn Reson. 2010;207:8\u201316. https:\/\/doi.org\/10.1016\/j.jmr.2010.07.016.","journal-title":"J Magn Reson"},{"key":"3522_CR12","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.abb.2017.05.011","volume":"628","author":"SJ Opella","year":"2017","unstructured":"Opella SJ, Marassi FM. Applications of NMR to membrane proteins. Arch Biochem Biophys. 2017;628:92\u2013101. https:\/\/doi.org\/10.1016\/j.abb.2017.05.011.","journal-title":"Arch Biochem Biophys"},{"issue":"1","key":"3522_CR13","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1007\/s10858-016-0082-5","volume":"67","author":"Y Tian","year":"2017","unstructured":"Tian Y, Schwieters CD, Opella SJ, Marassi FM. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH. J Biomol NMR. 2017;67(1):35\u201349. https:\/\/doi.org\/10.1007\/s10858-016-0082-5.","journal-title":"J Biomol NMR"},{"key":"3522_CR14","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.jmr.2014.11.015","volume":"253","author":"SJ Opella","year":"2015","unstructured":"Opella SJ. Solid-state NMR and membrane proteins. J Magn Reson. 2015;253:129\u201337. https:\/\/doi.org\/10.1016\/j.jmr.2014.11.015.","journal-title":"J Magn Reson"},{"key":"3522_CR15","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.jmr.2008.01.014","volume":"192","author":"S Bansal","year":"2008","unstructured":"Bansal S, Miao X, Adams MWW, Prestegard JH, Valafar H. Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA). J Magn Reson. 2008;192:60\u20138. https:\/\/doi.org\/10.1016\/j.jmr.2008.01.014.","journal-title":"J Magn Reson"},{"key":"3522_CR16","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1016\/S0959-440X(00)00245-1","volume":"11","author":"JR Tolman","year":"2001","unstructured":"Tolman JR. Dipolar couplings as a probe of molecular dynamics and structure in solution. Curr Opin Struct Biol. 2001;11:532\u20139.","journal-title":"Curr Opin Struct Biol"},{"key":"3522_CR17","doi-asserted-by":"publisher","first-page":"1416","DOI":"10.1021\/ja002500y","volume":"123","author":"JR Tolman","year":"2001","unstructured":"Tolman JR, Al-Hashimi HM, Kay LE, Prestegard JH. Structural and dynamic analysis of residual dipolar coupling data for proteins. J Am Chem Soc. 2001;123:1416\u201324.","journal-title":"J Am Chem Soc"},{"key":"3522_CR18","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1038\/nature03199","volume":"433","author":"K Lindorff-Larsen","year":"2005","unstructured":"Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M. Simultaneous determination of protein structure and dynamics. Nature. 2005;433:128\u201332. https:\/\/doi.org\/10.1038\/nature03199.","journal-title":"Nature"},{"key":"3522_CR19","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.pnmrs.2004.11.002","volume":"46","author":"M Blackledge","year":"2005","unstructured":"Blackledge M. Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings. Prog Nucl Magn Reson Spectrosc. 2005;46:23\u201361. https:\/\/doi.org\/10.1016\/j.pnmrs.2004.11.002.","journal-title":"Prog Nucl Magn Reson Spectrosc"},{"key":"3522_CR20","doi-asserted-by":"publisher","first-page":"1901","DOI":"10.1002\/cphc.200700353","volume":"8","author":"G Bouvignies","year":"2007","unstructured":"Bouvignies G, Markwick PRL, Blackledge M. Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings. Chemphyschem. 2007;8:1901\u20139. https:\/\/doi.org\/10.1002\/cphc.200700353.","journal-title":"Chemphyschem"},{"key":"3522_CR21","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1021\/acs.jctc.5b01091","volume":"12","author":"CA Cole","year":"2016","unstructured":"Cole CA, Mukhopadhyay R, Omar H, Hennig M, Valafar H. Structure calculation and reconstruction of discrete-state dynamics from residual dipolar couplings. J Chem Theory Comput. 2016;12:1408\u201322. https:\/\/doi.org\/10.1021\/acs.jctc.5b01091.","journal-title":"J Chem Theory Comput"},{"key":"3522_CR22","doi-asserted-by":"publisher","first-page":"6270","DOI":"10.1021\/jacs.5b01289","volume":"137","author":"S Olsson","year":"2015","unstructured":"Olsson S, Ekonomiuk D, Sgrignani J, Cavalli A. Molecular dynamics of biomolecules through direct analysis of dipolar couplings. J Am Chem Soc. 2015;137:6270\u20138.","journal-title":"J Am Chem Soc"},{"key":"3522_CR23","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1107\/S1399004713034160","volume":"70","author":"M Rinaldelli","year":"2014","unstructured":"Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement\/detection of structural differences. Acta crystallographica Section D Biological crystallography. 2014;70:958\u201367. https:\/\/doi.org\/10.1107\/S1399004713034160.","journal-title":"Acta crystallographica Section D Biological crystallography"},{"key":"3522_CR24","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1007\/s10858-012-9644-3","volume":"53","author":"RW Montalvao","year":"2012","unstructured":"Montalvao RW, Simone AD, Vendruscolo M. Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings. J Biomol NMR. 2012;53:281\u201392. https:\/\/doi.org\/10.1007\/s10858-012-9644-3.","journal-title":"J Biomol NMR"},{"key":"3522_CR25","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1007\/s10858-014-9871-x","volume":"60","author":"M Simin","year":"2014","unstructured":"Simin M, Irausquin S, Cole CA, Valafar H. Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. J Biomol NMR. 2014;60:241\u201364. https:\/\/doi.org\/10.1007\/s10858-014-9871-x.","journal-title":"J Biomol NMR"},{"key":"3522_CR26","doi-asserted-by":"publisher","first-page":"1541","DOI":"10.1021\/ja005590f","volume":"123","author":"J-C Hus","year":"2001","unstructured":"Hus J-C, Marion D, Blackledge M. Determination of protein backbone structure using only residual dipolar couplings. J Am Chem Soc. 2001;123:1541\u20132.","journal-title":"J Am Chem Soc"},{"key":"3522_CR27","doi-asserted-by":"publisher","first-page":"2142","DOI":"10.1021\/ja993603n","volume":"122","author":"F Delaglio","year":"2000","unstructured":"Delaglio F, Kontaxis G, Bax A. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J Am Chem Soc. 2000;122:2142\u20133. https:\/\/doi.org\/10.1021\/ja993603n.","journal-title":"J Am Chem Soc"},{"key":"3522_CR28","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1023\/A:1013334513610","volume":"21","author":"M Andrec","year":"2001","unstructured":"Andrec M, Du P, Levy RM. Protein backbone structure determination using only residual dipolar couplings from one ordering medium. J Biomol NMR. 2001;21:335\u201347. https:\/\/doi.org\/10.1023\/A:1013334513610.","journal-title":"J Biomol NMR"},{"key":"3522_CR29","doi-asserted-by":"publisher","first-page":"9614","DOI":"10.1021\/acs.jpcb.5b03859","volume":"119","author":"S Yang","year":"2015","unstructured":"Yang S, Al-Hashimi HM. Unveiling inherent degeneracies in determining population-weighted ensembles of Interdomain Orientational distributions using NMR residual dipolar couplings: application to RNA Helix junction Helix motifs. J Phys Chem B. 2015;119:9614\u201326.","journal-title":"J Phys Chem B"},{"key":"3522_CR30","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/128_2011_215","volume":"326","author":"K Chen","year":"2012","unstructured":"Chen K, Tjandra N. The use of residual dipolar coupling in studying proteins by NMR. Top Curr Chem. 2012;326:47\u201367. https:\/\/doi.org\/10.1007\/128_2011_215.","journal-title":"Top Curr Chem"},{"key":"3522_CR31","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/s10858-009-9366-3","volume":"45","author":"J Zeng","year":"2009","unstructured":"Zeng J, et al. High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations. J Biomol NMR. 2009;45:265\u201381.","journal-title":"J Biomol NMR"},{"key":"3522_CR32","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.pnmrs.2005.10.001","volume":"48","author":"C SCHWIETERS","year":"2006","unstructured":"SCHWIETERS C, KUSZEWSKI J, MARIUSCLORE G. Using Xplor\u2013NIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc. 2006;48:47\u201362. https:\/\/doi.org\/10.1016\/j.pnmrs.2005.10.001.","journal-title":"Prog Nucl Magn Reson Spectrosc"},{"key":"3522_CR33","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/s10858-010-9467-z","volume":"49","author":"X Wang","year":"2011","unstructured":"Wang X, Tash B, Flanagan JM, Tian F. RDC derived protein backbone resonance assignment using fragment assembly. J Biomol NMR. 2011;49:85\u201398. https:\/\/doi.org\/10.1007\/s10858-010-9467-z.","journal-title":"J Biomol NMR"},{"key":"3522_CR34","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1038\/nsmb.3041","volume":"22","author":"A Gutmanas","year":"2015","unstructured":"Gutmanas A, et al. NMR exchange format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol. 2015;22:433\u20134. https:\/\/doi.org\/10.1038\/nsmb.3041.","journal-title":"Nat Struct Mol Biol"},{"key":"3522_CR35","volume-title":"\u201cPDBMine: A Reformulation of the Protein Data Bank to Facilitate Structural Data Mining,\u201d presented at the IEEE Annual Conf. on Computational Science & Computational Intelligence (CSCI), Las Vegas, NV, December 5th\u20137th, 2019","author":"CA Cole","year":"2019","unstructured":"Cole CA, Ott C, Valdes D, Valafar H. \u201cPDBMine: A Reformulation of the Protein Data Bank to Facilitate Structural Data Mining,\u201d presented at the IEEE Annual Conf. on Computational Science & Computational Intelligence (CSCI), Las Vegas, NV, December 5th\u20137th, 2019; 2019."},{"key":"3522_CR36","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/S0022-2836(63)80023-6","volume":"7","author":"GN Ramachandran","year":"1963","unstructured":"Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963;7:95\u20139. https:\/\/doi.org\/10.1016\/S0022-2836(63)80023-6.","journal-title":"J Mol Biol"},{"key":"3522_CR37","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1103\/PhysRevLett.11.462","volume":"11","author":"A Saupe","year":"1963","unstructured":"Saupe A, Englert G. High-resolution nuclear magnetic resonance spectra of orientated molecules. Phys Rev Lett. 1963;11:462\u20134. https:\/\/doi.org\/10.1103\/PhysRevLett.11.462.","journal-title":"Phys Rev Lett"},{"key":"3522_CR38","volume-title":"Alignment Media Preparation","author":"H Lee","year":"2013","unstructured":"H. Lee, P. K, S. T, G. T. Montelione, and J. H. Prestegard, \"Alignment Media Preparation,\" 2013."},{"key":"3522_CR39","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/S0076-6879(01)39313-8","volume":"339","author":"A Bax","year":"2001","unstructured":"Bax A, Kontaxis G, Tjandra N. Dipolar couplings in macromolecular structure determination. Methods Enzymol. 2001;339:127\u201374.","journal-title":"Methods Enzymol"},{"key":"3522_CR40","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1007\/s10858-007-9168-4","volume":"38","author":"K Chen","year":"2007","unstructured":"Chen K, Tjandra N. Top-down approach in protein RDC data analysis: de novo estimation of the alignment tensor. J Biomol NMR. 2007;38:303\u201313. https:\/\/doi.org\/10.1007\/s10858-007-9168-4.","journal-title":"J Biomol NMR"},{"key":"3522_CR41","doi-asserted-by":"publisher","first-page":"Artn 052021","DOI":"10.1088\/1742-6596\/396\/5\/052021","volume":"396","author":"M Clemencic","year":"2012","unstructured":"Clemencic M, Mato P. A CMake-based build and configuration framework. (in English), J Phys Conf Ser. 2012;396:Artn 052021. https:\/\/doi.org\/10.1088\/1742-6596\/396\/5\/052021.","journal-title":"(in English), J Phys Conf Ser"},{"issue":"1","key":"3522_CR42","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28(1):235\u201342. https:\/\/doi.org\/10.1093\/nar\/28.1.235.","journal-title":"Nucleic Acids Res"},{"key":"3522_CR43","doi-asserted-by":"publisher","first-page":"2923","DOI":"10.1021\/ja0386804","volume":"126","author":"GM Clore","year":"2004","unstructured":"Clore GM, Schwieters CD. How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J Am Chem Soc. 2004;126:2923\u201338.","journal-title":"J Am Chem Soc"},{"key":"3522_CR44","doi-asserted-by":"publisher","first-page":"e1002035","DOI":"10.1371\/journal.pcbi.1002035","volume":"7","author":"D Long","year":"2011","unstructured":"Long D, Br\u00fcschweiler R. In silico elucidation of the recognition dynamics of ubiquitin. PLoS Comput Biol. 2011;7:e1002035. https:\/\/doi.org\/10.1371\/journal.pcbi.1002035.","journal-title":"PLoS Comput Biol"},{"key":"3522_CR45","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1002\/prot.23207","volume":"80","author":"C Tripathy","year":"2012","unstructured":"Tripathy C, Zeng J, Zhou P, Donald BR. Protein loop closure using orientational restraints from NMR data. Proteins. 2012;80:433\u201353.","journal-title":"Proteins"},{"issue":"10","key":"3522_CR46","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1007\/s00214-013-1388-y","volume":"132","author":"BL Eggimann","year":"2013","unstructured":"Eggimann BL, Vostrikov VV, Veglia G, Siepmann JI. Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field. Theor Chem Accounts. 2013;132(10):1388. https:\/\/doi.org\/10.1007\/s00214-013-1388-y.","journal-title":"Theor Chem Accounts"},{"key":"3522_CR47","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1385\/1-59259-809-9:089","volume":"278","author":"E de Alba","year":"2004","unstructured":"de Alba E, Tjandra N. Residual dipolar couplings in protein structure determination. Methods Mol Biol. 2004;278:89\u2013106. https:\/\/doi.org\/10.1385\/1-59259-809-9:089.","journal-title":"Methods Mol Biol"},{"key":"3522_CR48","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.jmr.2009.02.014","volume":"198","author":"R Mukhopadhyay","year":"2009","unstructured":"Mukhopadhyay R, Miao X, Shealy P, Valafar H. Efficient and accurate estimation of relative order tensors from lambda-maps. J Magn Reson (San Diego, Calif : 1997). 2009;198:236\u201347. https:\/\/doi.org\/10.1016\/j.jmr.2009.02.014.","journal-title":"J Magn Reson (San Diego, Calif : 1997)"},{"key":"3522_CR49","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2105-14-302","volume":"14","author":"C Schmidt","year":"2013","unstructured":"Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. BMC bioinformatics. 2013;14:302. https:\/\/doi.org\/10.1186\/1471-2105-14-302.","journal-title":"BMC bioinformatics"},{"key":"3522_CR50","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1186\/1471-2105-13-105","volume":"13","author":"P Shealy","year":"2012","unstructured":"Shealy P, Valafar H. Multiple structure alignment with msTALI. BMC bioinformatics. 2012;13:105. https:\/\/doi.org\/10.1186\/1471-2105-13-105.","journal-title":"BMC bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-3522-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-020-3522-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-3522-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,3]],"date-time":"2020-12-03T10:04:54Z","timestamp":1606989894000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-020-3522-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12]]},"references-count":50,"journal-issue":{"issue":"S9","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3522"],"URL":"https:\/\/doi.org\/10.1186\/s12859-020-3522-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2020,12]]},"assertion":[{"value":"16 April 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 April 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 December 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not Applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not Applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"204"}}