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Results: 1 to 20 of 320

1.

Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications.

Chiu HJ, Grant JC, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.

Acta Crystallogr D Biol Crystallogr. 2014 Oct 1;70(Pt 10):2640-51. doi: 10.1107/S1399004714017052. Epub 2014 Sep 27.

PMID:
25286848
[PubMed - in process]
2.

Basis for substrate recognition and distinction by matrix metalloproteinases.

Ratnikov BI, Cieplak P, Gramatikoff K, Pierce J, Eroshkin A, Igarashi Y, Kazanov M, Sun Q, Godzik A, Osterman A, Stec B, Strongin A, Smith JW.

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4148-55. doi: 10.1073/pnas.1406134111. Epub 2014 Sep 22.

PMID:
25246591
[PubMed - in process]
3.

Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models.

Hwang WC, Golden JW, Pascual J, Xu D, Cheltsov A, Godzik A.

Proteins. 2014 Sep 1. doi: 10.1002/prot.24679. [Epub ahead of print]

PMID:
25179344
[PubMed - as supplied by publisher]
4.

Phylogenomic analysis of glycogen branching and debranching enzymatic duo.

Zmasek CM, Godzik A.

BMC Evol Biol. 2014 Aug 23;14:183. doi: 10.1186/s12862-014-0183-2.

PMID:
25148856
[PubMed - in process]
Free Article
5.

Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50.

Hwang WC, Xu Q, Wu B, Godzik A.

Proteins. 2014 Aug 5. doi: 10.1002/prot.24661. [Epub ahead of print]

PMID:
25092800
[PubMed - as supplied by publisher]
6.

e-Driver: a novel method to identify protein regions driving cancer.

Porta-Pardo E, Godzik A.

Bioinformatics. 2014 Nov 1;30(21):3109-14. doi: 10.1093/bioinformatics/btu499. Epub 2014 Jul 26.

PMID:
25064568
[PubMed - in process]
7.

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.

Protein Sci. 2014 Oct;23(10):1380-91. doi: 10.1002/pro.2522. Epub 2014 Aug 12.

PMID:
25044324
[PubMed - in process]
8.

S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death.

Okamoto S, Nakamura T, Cieplak P, Chan SF, Kalashnikova E, Liao L, Saleem S, Han X, Clemente A, Nutter A, Sances S, Brechtel C, Haus D, Haun F, Sanz-Blasco S, Huang X, Li H, Zaremba JD, Cui J, Gu Z, Nikzad R, Harrop A, McKercher SR, Godzik A, Yates JR 3rd, Lipton SA.

Cell Rep. 2014 Jul 10;8(1):217-28. doi: 10.1016/j.celrep.2014.06.005. Epub 2014 Jul 4.

PMID:
25001280
[PubMed - in process]
Free Article
9.

PubServer: literature searches by homology.

Jaroszewski L, Koska L, Sedova M, Godzik A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W430-5. doi: 10.1093/nar/gku450. Epub 2014 Jun 23.

PMID:
24957597
[PubMed - indexed for MEDLINE]
Free Article
10.

Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.

Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A.

BMC Bioinformatics. 2014 Jun 17;15:196. doi: 10.1186/1471-2105-15-196.

PMID:
24938123
[PubMed - in process]
Free PMC Article
11.

Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.

Fleischman NM, Das D, Kumar A, Xu Q, Chiu HJ, Jaroszewski L, Knuth MW, Klock HE, Miller MD, Elsliger MA, Godzik A, Lesley SA, Deacon AM, Wilson IA, Toney MD.

Protein Sci. 2014 Aug;23(8):1060-76. doi: 10.1002/pro.2493. Epub 2014 Jun 14.

PMID:
24888348
[PubMed - in process]
12.

POSA: a user-driven, interactive multiple protein structure alignment server.

Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W240-5. doi: 10.1093/nar/gku394. Epub 2014 May 16.

PMID:
24838569
[PubMed - indexed for MEDLINE]
Free Article
13.

AIDA: ab initio domain assembly server.

Xu D, Jaroszewski L, Li Z, Godzik A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W308-13. doi: 10.1093/nar/gku369. Epub 2014 May 15.

PMID:
24831546
[PubMed - indexed for MEDLINE]
Free Article
14.

ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

Hrabe T, Godzik A.

BMC Bioinformatics. 2014 Apr 27;15:119. doi: 10.1186/1471-2105-15-119.

PMID:
24766872
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase.

Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A.

BMC Bioinformatics. 2014 Apr 17;15:112. doi: 10.1186/1471-2105-15-112.

PMID:
24742328
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.

Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L.

BMC Bioinformatics. 2014 Mar 19;15:75. doi: 10.1186/1471-2105-15-75.

PMID:
24646163
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Improving the chances of successful protein structure determination with a random forest classifier.

Jahandideh S, Jaroszewski L, Godzik A.

Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):627-35. doi: 10.1107/S1399004713032070. Epub 2014 Feb 15.

PMID:
24598732
[PubMed - indexed for MEDLINE]
18.

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.

Ravcheev DA, Godzik A, Osterman AL, Rodionov DA.

BMC Genomics. 2013 Dec 12;14:873. doi: 10.1186/1471-2164-14-873.

PMID:
24330590
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

LUD, a new protein domain associated with lactate utilization.

Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A.

BMC Bioinformatics. 2013 Nov 26;14:341. doi: 10.1186/1471-2105-14-341.

PMID:
24274019
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

bNAber: database of broadly neutralizing HIV antibodies.

Eroshkin AM, LeBlanc A, Weekes D, Post K, Li Z, Rajput A, Butera ST, Burton DR, Godzik A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1133-9. doi: 10.1093/nar/gkt1083. Epub 2013 Nov 7.

PMID:
24214957
[PubMed - indexed for MEDLINE]
Free PMC Article

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