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Items: 1 to 20 of 26

1.

Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism.

Pathak DT, Wei X, Bucuvalas A, Haft DH, Gerloff DL, Wall D.

PLoS Genet. 2012;8(4):e1002626. doi: 10.1371/journal.pgen.1002626.

3.

CharProtDB: a database of experimentally characterized protein annotations.

Madupu R, Richter A, Dodson RJ, Brinkac L, Harkins D, Durkin S, Shrivastava S, Sutton G, Haft D.

Nucleic Acids Res. 2012 Jan;40(Database issue):D237-41. doi: 10.1093/nar/gkr1133.

4.

The Pfam protein families database.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065.

5.

Chemistry and biology of the copper chelator methanobactin.

Kenney GE, Rosenzweig AC.

ACS Chem Biol. 2012 Feb 17;7(2):260-8. doi: 10.1021/cb2003913. Review.

6.

InterPro in 2011: new developments in the family and domain prediction database.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.

Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. doi: 10.1093/nar/gkr948.

7.

ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.

Basu MK, Selengut JD, Haft DH.

BMC Bioinformatics. 2011 Nov 9;12:434. doi: 10.1186/1471-2105-12-434.

8.

Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.

Haft DH, Payne SH, Selengut JD.

J Bacteriol. 2012 Jan;194(1):36-48. doi: 10.1128/JB.06026-11.

9.

HMMER web server: interactive sequence similarity searching.

Finn RD, Clements J, Eddy SR.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37. doi: 10.1093/nar/gkr367.

10.

Evolution and classification of the CRISPR-Cas systems.

Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV.

Nat Rev Microbiol. 2011 Jun;9(6):467-77. doi: 10.1038/nrmicro2577. Review.

11.
12.

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.

13.

A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.

Krentz BD, Mulheron HJ, Semrau JD, Dispirito AA, Bandow NL, Haft DH, Vuilleumier S, Murrell JC, McEllistrem MT, Hartsel SC, Gallagher WH.

Biochemistry. 2010 Nov 30;49(47):10117-30. doi: 10.1021/bi1014375.

14.

A new generation of homology search tools based on probabilistic inference.

Eddy SR.

Genome Inform. 2009 Oct;23(1):205-11.

PMID:
20180275
15.

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

Schnoes AM, Brown SD, Dodevski I, Babbitt PC.

PLoS Comput Biol. 2009 Dec;5(12):e1000605. doi: 10.1371/journal.pcbi.1000605.

16.

The comprehensive microbial resource.

Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5. doi: 10.1093/nar/gkp912.

17.

Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.

Haft DH, Self WT.

Biol Direct. 2008 Feb 20;3:4. doi: 10.1186/1745-6150-3-4.

18.

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.

Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O.

Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4.

19.
20.

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702.

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