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Page 1
Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.
Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY. Baskaran K, et al. Among authors: young jy. Structure. 2024 Mar 7:S0969-2126(24)00050-9. doi: 10.1016/j.str.2024.02.011. Online ahead of print. Structure. 2024. PMID: 38490206 Free article.
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. Young JY, et al. Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9. Structure. 2017. PMID: 28190782 Free PMC article.
Validation of Structures in the Protein Data Bank.
Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Gore S, et al. Among authors: young jy. Structure. 2017 Dec 5;25(12):1916-1927. doi: 10.1016/j.str.2017.10.009. Epub 2017 Nov 22. Structure. 2017. PMID: 29174494 Free PMC article.
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.
Feng Z, Westbrook JD, Sala R, Smart OS, Bricogne G, Matsubara M, Yamada I, Tsuchiya S, Aoki-Kinoshita KF, Hoch JC, Kurisu G, Velankar S, Burley SK, Young JY. Feng Z, et al. Among authors: young jy. Structure. 2021 Apr 1;29(4):393-400.e1. doi: 10.1016/j.str.2021.02.004. Epub 2021 Mar 2. Structure. 2021. PMID: 33657417 Free PMC article.
Simplified quality assessment for small-molecule ligands in the Protein Data Bank.
Shao C, Westbrook JD, Lu C, Bhikadiya C, Peisach E, Young JY, Duarte JM, Lowe R, Wang S, Rose Y, Feng Z, Burley SK. Shao C, et al. Among authors: young jy. Structure. 2022 Feb 3;30(2):252-262.e4. doi: 10.1016/j.str.2021.10.003. Epub 2022 Jan 12. Structure. 2022. PMID: 35026162 Free PMC article.
Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank.
Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY. Baskaran K, et al. Among authors: young jy. bioRxiv [Preprint]. 2024 Jan 22:2024.01.15.575520. doi: 10.1101/2024.01.15.575520. bioRxiv. 2024. PMID: 38328042 Free PMC article. Updated. Preprint.
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Adams PD, et al. Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017. Structure. 2016. PMID: 27050687 Free PMC article.
DCC: a Swiss army knife for structure factor analysis and validation.
Yang H, Peisach E, Westbrook JD, Young J, Berman HM, Burley SK. Yang H, et al. J Appl Crystallogr. 2016 Apr 18;49(Pt 3):1081-1084. doi: 10.1107/S1600576716004428. eCollection 2016 Jun 1. J Appl Crystallogr. 2016. PMID: 27275151 Free PMC article.
54 results