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Results: 1 to 20 of 326


Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells.

Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4666-71. doi: 10.1073/pnas.1502855112. Epub 2015 Mar 30.


AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.

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

Bioinformatics. 2015 Feb 19. pii: btv092. [Epub ahead of print]


Analysis of individual protein regions provides novel insights on cancer pharmacogenomics.

Porta Pardo E, Godzik A.

PLoS Comput Biol. 2015 Jan 8;11(1):e1004024. doi: 10.1371/journal.pcbi.1004024. eCollection 2015 Jan.


Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.

Xu Q, Mengin-Lecreulx D, Patin D, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA.

Structure. 2014 Dec 2;22(12):1799-809. doi: 10.1016/j.str.2014.09.018. Epub 2014 Nov 20.


Cancer3D: understanding cancer mutations through protein structures.

Porta-Pardo E, Hrabe T, Godzik A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D968-73. doi: 10.1093/nar/gku1140. Epub 2014 Nov 11.


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;70(Pt 10):2640-51. doi: 10.1107/S1399004714017052. Epub 2014 Sep 27.


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.


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]


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.


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]


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.


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.


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.


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.


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.


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.


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.


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.


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.

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