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Results: 1 to 20 of 316

1.

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]
2.

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

Porta-Pardo E, Godzik A.

Bioinformatics. 2014 Jul 26. pii: btu499. [Epub ahead of print]

PMID:
25064568
[PubMed - as supplied by publisher]
3.

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 Jul 16. doi: 10.1002/pro.2522. [Epub ahead of print]

PMID:
25044324
[PubMed - as supplied by publisher]
4.

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
5.

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 - in process]
Free Article
6.

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
7.

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]
8.

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 - in process]
Free Article
9.

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 - in process]
Free Article
10.

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
11.

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
12.

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
13.

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]
14.

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 - in process]
Free PMC Article
15.

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
16.

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
17.

Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family.

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

Proteins. 2014 Jun;82(6):1086-92. doi: 10.1002/prot.24455. Epub 2013 Nov 22.

PMID:
24174223
[PubMed - in process]
18.

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.

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

Bioinformatics. 2014 Mar 1;30(5):660-7. doi: 10.1093/bioinformatics/btt578. Epub 2013 Oct 15.

PMID:
24130308
[PubMed - indexed for MEDLINE]
19.

Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling.

Das D, Hervé M, Elsliger MA, Kadam RU, Grant JC, Chiu HJ, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IA.

J Bacteriol. 2013 Dec;195(24):5555-66. doi: 10.1128/JB.00900-13. Epub 2013 Oct 11.

PMID:
24123814
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE.

Nat Struct Mol Biol. 2013 Nov;20(11):1243-9. doi: 10.1038/nsmb.2676. Epub 2013 Sep 29.

PMID:
24077226
[PubMed - indexed for MEDLINE]
Free PMC Article

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