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MMDB: Entrez's 3D-structure database.
Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. Chen J, et al. Among authors: jackson jd. Nucleic Acids Res. 2003 Jan 1;31(1):474-7. doi: 10.1093/nar/gkg086. Nucleic Acids Res. 2003. PMID: 12520055 Free PMC article.
CDD: a curated Entrez database of conserved domain alignments.
Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. Marchler-Bauer A, et al. Among authors: jackson jd. Nucleic Acids Res. 2003 Jan 1;31(1):383-7. doi: 10.1093/nar/gkg087. Nucleic Acids Res. 2003. PMID: 12520028 Free PMC article.
CDD: a Conserved Domain Database for protein classification.
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. Marchler-Bauer A, et al. Among authors: jackson jd. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6. doi: 10.1093/nar/gki069. Nucleic Acids Res. 2005. PMID: 15608175 Free PMC article.
CDD: a conserved domain database for interactive domain family analysis.
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. Marchler-Bauer A, et al. Among authors: jackson jd. Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40. doi: 10.1093/nar/gkl951. Epub 2006 Nov 29. Nucleic Acids Res. 2007. PMID: 17135202 Free PMC article.
CDD: specific functional annotation with the Conserved Domain Database.
Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. Marchler-Bauer A, et al. Among authors: jackson jd. Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10. doi: 10.1093/nar/gkn845. Epub 2008 Nov 4. Nucleic Acids Res. 2009. PMID: 18984618 Free PMC article.
CDD: a Conserved Domain Database for the functional annotation of proteins.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. Marchler-Bauer A, et al. Among authors: jackson jd. Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9. doi: 10.1093/nar/gkq1189. Epub 2010 Nov 24. Nucleic Acids Res. 2011. PMID: 21109532 Free PMC article.
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. Tatusov RL, et al. Among authors: jackson jd. BMC Bioinformatics. 2003 Sep 11;4:41. doi: 10.1186/1471-2105-4-41. Epub 2003 Sep 11. BMC Bioinformatics. 2003. PMID: 12969510 Free PMC article.
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. Koonin EV, et al. Among authors: jackson jd. Genome Biol. 2004;5(2):R7. doi: 10.1186/gb-2004-5-2-r7. Epub 2004 Jan 15. Genome Biol. 2004. PMID: 14759257 Free PMC article.
Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.
Rogozin IB, Babenko VN, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Mirkin BG, Nikolskaya AN, Rao BS, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA, Koonin EV. Rogozin IB, et al. Among authors: jackson jd. Cold Spring Harb Symp Quant Biol. 2003;68:293-301. doi: 10.1101/sqb.2003.68.293. Cold Spring Harb Symp Quant Biol. 2003. PMID: 15338629 No abstract available.
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.
Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD. Pujar S, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D221-D228. doi: 10.1093/nar/gkx1031. Nucleic Acids Res. 2018. PMID: 29126148 Free PMC article.
234 results