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Items: 1 to 50 of 350

1.

Structures of single-layer β-sheet proteins evolved from β-hairpin repeats.

Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA.

Protein Sci. 2019 Sep;28(9):1676-1689. doi: 10.1002/pro.3683. Epub 2019 Aug 2.

PMID:
31306512
2.

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets.

Sedova M, Iyer M, Li Z, Jaroszewski L, Post KW, Hrabe T, Porta-Pardo E, Godzik A.

Nucleic Acids Res. 2019 Jan 8;47(D1):D895-D899. doi: 10.1093/nar/gky1098.

3.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. No abstract available.

4.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035.

5.

Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.

Trinh SA, Leyn SA, Rodionov ID, Godzik A, Satchell KJF.

Genome Announc. 2018 Jan 18;6(3). pii: e01387-17. doi: 10.1128/genomeA.01387-17.

6.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y. Review.

7.

The Functional Impact of Alternative Splicing in Cancer.

Climente-González H, Porta-Pardo E, Godzik A, Eyras E.

Cell Rep. 2017 Aug 29;20(9):2215-2226. doi: 10.1016/j.celrep.2017.08.012.

8.

Comparison of algorithms for the detection of cancer drivers at subgene resolution.

Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A.

Nat Methods. 2017 Aug;14(8):782-788. doi: 10.1038/nmeth.4364. Epub 2017 Jul 17.

9.

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

Derewenda ZS, Godzik A.

Methods Mol Biol. 2017;1607:77-115. doi: 10.1007/978-1-4939-7000-1_4. Review.

10.

Mutation Drivers of Immunological Responses to Cancer.

Porta-Pardo E, Godzik A.

Cancer Immunol Res. 2016 Sep 2;4(9):789-98. doi: 10.1158/2326-6066.CIR-15-0233. Epub 2016 Jul 11.

11.

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination.

Braten O, Livneh I, Ziv T, Admon A, Kehat I, Caspi LH, Gonen H, Bercovich B, Godzik A, Jahandideh S, Jaroszewski L, Sommer T, Kwon YT, Guharoy M, Tompa P, Ciechanover A.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):E4639-47. doi: 10.1073/pnas.1608644113. Epub 2016 Jul 6.

12.

Revealing aperiodic aspects of solenoid proteins from sequence information.

Hrabe T, Jaroszewski L, Godzik A.

Bioinformatics. 2016 Sep 15;32(18):2776-82. doi: 10.1093/bioinformatics/btw319. Epub 2016 Jun 9.

13.

Neutralizing antibody affords comparable protection against vaginal and rectal simian/human immunodeficiency virus challenge in macaques.

Moldt B, Le KM, Carnathan DG, Whitney JB, Schultz N, Lewis MG, Borducchi EN, Smith KM, Mackel JJ, Sweat SL, Hodges AP, Godzik A, Parren PW, Silvestri G, Barouch DH, Burton DR.

AIDS. 2016 Jun 19;30(10):1543-51. doi: 10.1097/QAD.0000000000001102.

14.

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

Serrano P, Dutta SK, Proudfoot A, Mohanty B, Susac L, Martin B, Geralt M, Jaroszewski L, Godzik A, Elsliger M, Wilson IA, Wüthrich K.

FEBS J. 2016 Nov;283(21):3870-3881. doi: 10.1111/febs.13751. Epub 2016 Jun 9.

15.

A Distinct Type of Pilus from the Human Microbiome.

Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA.

Cell. 2016 Apr 21;165(3):690-703. doi: 10.1016/j.cell.2016.03.016. Epub 2016 Apr 7.

16.

UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.

Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR.

Acta Crystallogr D Struct Biol. 2016 Apr;72(Pt 4):497-511. doi: 10.1107/S2059798316001248. Epub 2016 Mar 24.

17.

Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.

McLuskey K, Grewal JS, Das D, Godzik A, Lesley SA, Deacon AM, Coombs GH, Elsliger MA, Wilson IA, Mottram JC.

J Biol Chem. 2016 Apr 29;291(18):9482-91. doi: 10.1074/jbc.M115.706143. Epub 2016 Mar 3.

18.

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort.

Landais E, Huang X, Havenar-Daughton C, Murrell B, Price MA, Wickramasinghe L, Ramos A, Bian CB, Simek M, Allen S, Karita E, Kilembe W, Lakhi S, Inambao M, Kamali A, Sanders EJ, Anzala O, Edward V, Bekker LG, Tang J, Gilmour J, Kosakovsky-Pond SL, Phung P, Wrin T, Crotty S, Godzik A, Poignard P.

PLoS Pathog. 2016 Jan 14;12(1):e1005369. doi: 10.1371/journal.ppat.1005369. eCollection 2016 Jan.

19.

PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB.

Jahandideh S, Sharifi F, Jaroszewski L, Godzik A.

Source Code Biol Med. 2015 Dec 3;10:15. doi: 10.1186/s13029-015-0047-1. eCollection 2015.

20.

PDBFlex: exploring flexibility in protein structures.

Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D423-8. doi: 10.1093/nar/gkv1316. Epub 2015 Nov 28.

21.

Protael: protein data visualization library for the web.

Sedova M, Jaroszewski L, Godzik A.

Bioinformatics. 2016 Feb 15;32(4):602-4. doi: 10.1093/bioinformatics/btv605. Epub 2015 Oct 29.

22.

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.

Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A.

PLoS Comput Biol. 2015 Oct 20;11(10):e1004518. doi: 10.1371/journal.pcbi.1004518. eCollection 2015 Oct.

23.

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains.

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

MBio. 2015 Sep 15;6(5):e02327-14. doi: 10.1128/mBio.02327-14.

24.

Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus.

Dutta SK, Serrano P, Geralt M, Axelrod HL, Xu Q, Lesley SA, Godzik A, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K.

Protein Sci. 2015 Oct;24(10):1600-8. doi: 10.1002/pro.2743. Epub 2015 Jul 30.

25.

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.

26.

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 Jul 1;31(13):2098-105. doi: 10.1093/bioinformatics/btv092. Epub 2015 Feb 19.

27.
28.

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.

29.

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):1799-1809. doi: 10.1016/j.str.2014.09.018. Epub 2014 Nov 20.

30.

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.

31.

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.

32.

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.

33.

Retracted: 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] Retraction in: Proteins. ;86(2):268.

PMID:
25179344
34.

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.

35.

Retracted: 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] Retraction in: Proteins. ;86(2):269.

PMID:
25092800
36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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