{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:12:32Z","timestamp":1772172752661,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008060","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,11]],"date-time":"2021-02-11T00:00:00Z","timestamp":1613001600000}}],"reference-count":101,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"vor","delay-in-days":0,"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"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01GM120574"],"award-info":[{"award-number":["1R01GM120574"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Nuclear Magnetic Resonance (NMR) spectroscopy is one of the three primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by solution NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination from Residual Dipolar Couplings (RDCs) is relatively less well developed. Here, we describe the new features of the protein structure modeling program REDCRAFT and focus on the new Adaptive Decimation (AD) feature. The AD plays a critical role in improving the robustness of REDCRAFT to missing or noisy data, while allowing structure determination of larger proteins from less data. In this report we demonstrate the successful application of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data, and of larger proteins (145 to 573 residues) using simulated RDC data. In both cases, REDCRAFT uses only RDC data that can be collected from perdeuterated proteins. Finally, we compare the accuracy of structure determination from RDCs alone with traditional NOE-based methods for the structurally novel PF.2048.1 protein. The RDC-based structure of PF.2048.1 exhibited 1.0 \u00c5 BB-RMSD with respect to a high-quality NOE-based structure. Although optimal strategies would include using RDC data together with chemical shift, NOE, and other NMR data, these studies provide proof-of-principle for robust structure determination of largely-perdeuterated proteins from RDC data alone using REDCRAFT.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008060","type":"journal-article","created":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T17:24:57Z","timestamp":1612200297000},"page":"e1008060","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0320-6894","authenticated-orcid":true,"given":"Casey A.","family":"Cole","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3153-6583","authenticated-orcid":true,"given":"Nourhan S.","family":"Daigham","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4343-0356","authenticated-orcid":true,"given":"Gaohua","family":"Liu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9440-3059","authenticated-orcid":true,"given":"Gaetano T.","family":"Montelione","sequence":"additional","affiliation":[]},{"given":"Homayoun","family":"Valafar","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2021,2,1]]},"reference":[{"issue":"1","key":"pcbi.1008060.ref001","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"HM Berman","year":"2002","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"1","key":"pcbi.1008060.ref002","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008060.ref003","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gki057","article-title":"The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema","volume":"33","author":"N Deshpande","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008060.ref004","author":"NA Greshenfeld","year":"1998","journal-title":"The Nature of Mathematical Modeling"},{"key":"pcbi.1008060.ref005","first-page":"329","volume":"24","author":"WH Press","year":"2003","journal-title":"Numerical Recipes in C++: The Art of Scientific Computing (2nd edn) 1 Numerical Recipes Example Book (C++) (2nd edn) 2 Numerical Recipes Multi-Language Code CD ROM with LINUX or UNIX Single-Screen License Revised Version 3. 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