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Items: 1 to 20 of 25

1.

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.

Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D200-D203. doi: 10.1093/nar/gkw1129.

2.

CDD: NCBI's conserved domain database.

Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH.

Nucleic Acids Res. 2015 Jan;43(Database issue):D222-6. doi: 10.1093/nar/gku1221.

3.

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D297-303. doi: 10.1093/nar/gkt1208.

4.

CDD: conserved domains and protein three-dimensional structure.

Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D348-52. doi: 10.1093/nar/gks1243.

5.

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.

Neuwald AF, Lanczycki CJ, Marchler-Bauer A.

BMC Bioinformatics. 2012 Jun 22;13:144. doi: 10.1186/1471-2105-13-144.

6.

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W242-8. doi: 10.1093/nar/gks559.

7.

Annotation of functional sites with the Conserved Domain Database.

Derbyshire MK, Lanczycki CJ, Bryant SH, Marchler-Bauer A.

Database (Oxford). 2012 Mar 20;2012:bar058. doi: 10.1093/database/bar058.

8.

MMDB: 3D structures and macromolecular interactions.

Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH.

Nucleic Acids Res. 2012 Jan;40(Database issue):D461-4. doi: 10.1093/nar/gkr1162.

9.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9. doi: 10.1093/nar/gkq1189.

10.

Prediction of functionally important sites from protein sequences using sparse kernel least squares classifiers.

Tang K, Pugalenthi G, Suganthan PN, Lanczycki CJ, Chakrabarti S.

Biochem Biophys Res Commun. 2009 Jun 26;384(2):155-9. doi: 10.1016/j.bbrc.2009.04.096.

11.

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.

Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10. doi: 10.1093/nar/gkn845.

12.
13.

Analysis and prediction of functionally important sites in proteins.

Chakrabarti S, Lanczycki CJ.

Protein Sci. 2007 Jan;16(1):4-13.

14.

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.

Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40.

15.

State of the art: refinement of multiple sequence alignments.

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.

BMC Bioinformatics. 2006 Nov 14;7:499. Erratum in: BMC Bioinformatics. 2010;11:3.

16.

Refining multiple sequence alignments with conserved core regions.

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.

Nucleic Acids Res. 2006 May 17;34(9):2598-606.

17.

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.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6.

18.

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.

Nucleic Acids Res. 2003 Jan 1;31(1):474-7.

19.

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.

Nucleic Acids Res. 2003 Jan 1;31(1):383-7.

20.

Far from equilibrium nonconserved growth under a surface diffusion bias.

Lanczycki CJ, Jejjala V V, Das Sarma S.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Nov;54(5):4755-4759. No abstract available.

PMID:
9965654
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