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Page 1
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. Among authors: velankar s. 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.
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar… See abstract for full author list ➔ Lensink MF, et al. Among authors: velankar s. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.
Boutselakis H, Dimitropoulos D, Fillon J, Golovin A, Henrick K, Hussain A, Ionides J, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Oldfield T, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan J, Tagari M, Tate J, Tromm S, Velankar S, Vranken W. Boutselakis H, et al. Among authors: velankar s. Nucleic Acids Res. 2003 Jan 1;31(1):458-62. doi: 10.1093/nar/gkg065. Nucleic Acids Res. 2003. PMID: 12520052 Free PMC article.
E-MSD: an integrated data resource for bioinformatics.
Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K. Golovin A, et al. Among authors: velankar s. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D211-6. doi: 10.1093/nar/gkh078. Nucleic Acids Res. 2004. PMID: 14681397 Free PMC article.
E-MSD: improving data deposition and structure quality.
Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S. Tagari M, et al. Among authors: velankar s. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D287-90. doi: 10.1093/nar/gkj163. Nucleic Acids Res. 2006. PMID: 16381867 Free PMC article.
Remediation of the protein data bank archive.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. Henrick K, et al. Among authors: velankar s. Nucleic Acids Res. 2008 Jan;36(Database issue):D426-33. doi: 10.1093/nar/gkm937. Epub 2007 Dec 11. Nucleic Acids Res. 2008. PMID: 18073189 Free PMC article.
PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ. Velankar S, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D308-17. doi: 10.1093/nar/gkp916. Epub 2009 Oct 25. Nucleic Acids Res. 2010. PMID: 19858099 Free PMC article.
Straightforward and complete deposition of NMR data to the PDBe.
Penkett CJ, van Ginkel G, Velankar S, Swaminathan J, Ulrich EL, Mading S, Stevens TJ, Fogh RH, Gutmanas A, Kleywegt GJ, Henrick K, Vranken WF. Penkett CJ, et al. Among authors: velankar s. J Biomol NMR. 2010 Oct;48(2):85-92. doi: 10.1007/s10858-010-9439-3. Epub 2010 Aug 3. J Biomol NMR. 2010. PMID: 20680401 Free PMC article.
EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. Lawson CL, et al. Among authors: velankar s. Nucleic Acids Res. 2011 Jan;39(Database issue):D456-64. doi: 10.1093/nar/gkq880. Epub 2010 Oct 8. Nucleic Acids Res. 2011. PMID: 20935055 Free PMC article.
161 results