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Publications By Year

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2017>    To Top

Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A. Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nat Methods. 2017 Aug;14(8):782-788. PubMed

Derewenda ZS, Godzik A. The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol. 2017;1607:77-115. PubMed

Climente-González H, Porta-Pardo E, Godzik A., Eyras E. The Functional Impact of Alternative Splicing in Cancer. Cell Rep. 2017 Aug 29;20(9):2215-2226. PubMed

2016    To Top

Porta-Pardo E., Godzik A. Mutation drivers of immunological responses to cancer. Cancer Immunol Res. 2016 Jul 11. PubMed

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

Hrabe T, Jaroszewski L, Godzik A. Revealing aperiodic aspects of solenoid proteins from sequence information. Bioinformatics. 2016 Jun 9. PubMed

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. Neutralizing antibody affords comparable protection against vaginal and rectal simian/human immunodeficiency virus challenge in macaques. AIDS. 2016 Jun 19;30(10):1543-51. doi: 10.1097/QAD.0000000000001102. PubMed

Serrano P, Dutta SK, Proudfoot A, Mohanty B, Susac L, Martin B, Geralt M, Jaroszewski L, Godzik A, Elsliger M, Wilson IA, Wüthrich K. NMR in structural genomics to increase structural coverage of the protein universe. FEBS J. 2016 May 7. doi: 10.1111/febs.13751 PubMed

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. A Distinct Type of Pilus from the Human Microbiome. Cell. 2016 Apr 21;165(3):690-703. doi: 10.1016/j.cell.2016.03.016. Epub 2016 Apr 7. PubMed

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. UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol. 2016 Apr 1;72(Pt 4):497-511. doi: 10.1107/S2059798316001248. Epub 2016 Mar 24. PubMed

McLuskey K, Grewal JS, Das D, Godzik A, Lesley SA, Deacon AM, Coombs GH, Elsliger MA, Wilson IA, Mottram JC. Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome. J Biol Chem. 2016 Apr 29;291(18):9482-91. doi: 10.1074/jbc.M115.706143. Epub 2016 PubMed

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. Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort. PLoS Pathog. 2016 Jan 14;12(1):e1005369. doi: 10.1371/journal.ppat.1005369. PubMed

2015    To Top

Jahandideh S, Sharifi F, Jaroszewski L, Godzik A. PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source Code Biol Med. 2015 Dec 3;10:15. doi: 10.1186/s13029-015-0047-1. PubMed

Thomas Hrabe, Zhanwen Li, Mayya Sedova, Piotr Rotkiewicz, Lukasz Jaroszewski and Adam Godzik, PDBFlex: exploring flexibility in protein structures. Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv1316

Sedova M, Jaroszewski L, Godzik A. Protael: protein data visualization library for the web. Bioinformatics. 2015 Oct 29. pii: btv605. [Epub ahead of print] PubMed

Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput Biol. 2015 Oct 20;11(10):e1004518. doi: 10.1371/journal.pcbi.1004518. PubMed

Xu D, Jaroszewski L, Li Z,Godzik A. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinformatics. 2015 Feb 19. pii: btv092. [Epub ahead of print] PubMed

Natarajan P, Punta M, Kumar A, Yeh AP, Godzik A. Iyer AL. Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. BMC Bioinformatics. 2015 Jan 16;16(1):7. [Epub ahead of print] PubMed

Pardo-Pardo E.,Godzik A. Analysis of individual protein regions provides novel insights on cancer pharmacogenomics. PLoS Comput Biol. 2015 Jan 8;11(1):e1004024. doi: 10.1371/journal.pcbi.1004024. PubMed

2014    To Top

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-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family. Structure. 2014 Dec 2;22(12):1799-809. doi: 10.1016/j.str.2014.09.018. PubMed

Chiu HJ, Grant JC, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications. Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2640-51. doi: 10.1107/S1399004714017052. PubMed

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. Basis for substrate recognition and distinction by matrix metalloproteinases. Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4148-55. doi: 10.1073/pnas.1406134111. PubMed

Porta-Pardo E, Hrabe T and Godzik A. Cancer3D: understanding cancer mutations through protein structures. Nucl. Acids Res. (2014) doi: 10.1093/nar/gku1140. Download

Hwang WC, Golden JW, Pascual J, Xu D, Cheltsov A, Godzik A. Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models. Proteins. 2014 Sep 1. doi: 10.1002/prot.24679. [Epub ahead of print] PubMed

Zmasek CM, Godzik A. Phylogenomic analysis of glycogen branching and debranching enzymatic duo. BMC Evol Biol. 2014 Aug 23;14(1):183. [Epub ahead of print] PubMed

Hwang WC, Xu Q, Wu B, Godzik A. Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50. Proteins. 2014 Aug 5. doi: 10.1002/prot.24661. [Epub ahead of print] PubMed

Porta-Pardo E, Godzik A. e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics. 2014 Jul 26. doi:pii: btu499. [Epub ahead of print] PubMed

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. Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake. Protein Sci. 2014 Jul 16. doi: 10.1002/pro.2522. [Epub ahead of print] PubMed

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. S-nitrosylation-mediated redox transcriptional switch modulates neurogenesis and neuronal cell death. Cell Rep. 2014 Jul 10;8(1):217-28. doi: 10.1016/j.celrep.2014.06.005. Epub 2014 Jul 4. PubMed

Jaroszewski L, Koska L, Sedova M, Godzik A. PubServer: literature searches by homology. Nucleic Acids Res. 2014 Jun 23. doi:pii: gku450. [Epub ahead of print] PubMed

Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y, Godzik A. Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. BMC Bioinformatics. 2014 Jun 17;15:196. doi: 10.1186/1471-2105-15-196. PubMed

Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A. POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res. 2014 May 16. doi:pii: gku394. [Epub ahead of print] PubMed

Xu D, Jaroszewski L, Li Z, Godzik A. AIDA: ab initio domain assembly server. Nucleic Acids Res. 2014 May 15. doi:pii: gku369. [Epub ahead of print] PubMed

Hrabe T, Godzik A. ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures. BMC Bioinformatics. 2014 Apr 27;15(1):119. doi: 10.1186/1471-2105-15-119. PubMed

Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A. Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinformatics. 2014 Apr 17;15(1):112. doi: 10.1186/1471-2105-15-112. PubMed

Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A. Aravind L. 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. BMC Bioinformatics. 2014 Mar 19;15:75. doi: 10.1186/1471-2105-15-75. PubMed

Jahandideh S, Jaroszewski L, Godzik A. Improving the chances of successful protein structure determination with a random forest classifier. Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):627-35. doi: 10.1107/S1399004713032070. Epub 2014 Feb 15. PubMed

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. Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. Protein Sci. 2014 May 29. doi: 10.1002/pro.2493. [Epub ahead of print] PubMed

2013    To Top

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. LUD, a new protein domain associated with lactate utilization. BMC Bioinformatics. 2013 Nov 26;14:341. doi: 10.1186/1471-2105-14-341. PubMed

Eroshkin AM, Leblanc A, Weekes D, Post K, Li Z, Rajput A, Butera ST, Burton DR, Godzik A. bNAber: database of broadly neutralizing HIV antibodies. Nucleic Acids Res. 2013 Nov 7. PubMed

Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol. 2013 Nov;20(11):1243-9. doi: 10.1038/nsmb.2676. Epub 2013 Sep 29. PubMed

Xu D, Jaroszewski L, Li Z, Godzik A. FFAS-3D: Improving Fold Recognition by Including Optimized Structural Features and Template Re-ranking. Bioinformatics (2013) doi: 10.1093/bioinformatics/btt578 First published online: October 15, 2013 PubMed

Castellana NE, Lushnikov A, Rotkiewicz P, Sefcovic N, Pevzner PA, Godzik A, Vyatkina K. MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol Biol. (2013) Jul 11;8(1):19. doi: 10.1186/1748-7188-8-19. PubMed

Chang RL, Andrews K, Kim D, Li Z, Godzik A., Palsson BO. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science. 2013 Jun 7;340(6137):1220-3. doi: 10.1126/science.1234012. PubMed

Zmasek CM, Godzik A. Evolution of the animal apoptosis network. Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3):a008649. doi: 10.1101/cshperspect.a008649. PubMed

Zmasek CM, Godzik A. This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol. 2012;8(11):e1002701. doi: 10.1371/journal.pcbi.1002701. Epub 2012 Nov 15. PubMed

2012    To Top

Xu Q, van Wezel GP, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Correction: Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes. PLoS One. 2012;7(8). doi: 10.1371/annotation/f345da14-66b8-4e8b-b448-576dc29a03f5. Epub 2012 Aug 2. PubMed

Xu Q, van Wezel GP, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes. PLoS One. 2012;7(7):e41359. Epub 2012 Jul 26. PubMed

Xu Q, Gohler AK, Kosfeld A, Carlton D, Chiu HJ, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Jahreis K, Wilson IA. The structure of Mlc titration factor A (MtfA/YeeI) reveals a prototypical zinc metallopeptidase related to anthrax lethal factor. J Bacteriol. 2012 Jun;194(11):2987-99. Epub 2012 Mar 30. PubMed

Xu Q, Christen B, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Figurski DH, Shapiro L, Wilson IA. Structure of the pilus assembly protein TadZ from Eubacterium rectale: implications for polar localization. Mol Microbiol. 2012 Feb;83(4):712-27. doi: 10.1111/j.1365-2958.2011.07954.x. Epub 2012 Jan 18. PubMed

2011    To Top

Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Comput Biol. 2011 Dec;7(12):e1002318. Epub 2011 Dec 22. PubMed

D'Osualdo A, Weichenberger CX, Wagner RN, Godzik A, Wooley J, Reed JC. CARD8 and NLRP1 undergo autoproteolytic processing through a ZU5-like domain. PLoS One. 2011;6(11):e27396. Epub 2011 Nov 8. PubMed

Xu Q, Rawlings ND, Chiu HJ, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites. PLoS One. 2011;6(7):e22013. Epub 2011 Jul 22. PubMed

Xu Q, Rawlings ND, Farr CL, Chiu HJ, Grant JC, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake. PLoS One. 2011;6(7):e21875. Epub 2011 Jul 25. PubMed

Jaroszewski L, Li Z, Cai XH, Weber C, Godzik A. FFAS server: novel features and applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W38-44. PubMed

Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. Structural determinants of limited proteolysis. J Proteome Res. 2011 Aug 5;10(8):3642-51. Epub 2011 Jul 8. PubMed

Cai XH, Jaroszewski L, Wooley J, Godzik A. Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering. Proteins. 2011 Aug;79(8):2389-402. doi: 10.1002/prot.23049. Epub 2011 May 31. PubMed

Zakharov MN, Pillai BK, Bhasin S, Ulloor J, Istomin AY, Guo C, Godzik A, Kumar R, Jasuja R. Dynamics of coregulator-induced conformational perturbations in androgen receptor ligand binding domain. Mol Cell Endocrinol. 2011 Jul 20;341(1-2):1-8. Epub 2011 May 14. PubMed PMID: 21605623.

Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ. Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins. 2011 Jul;79(7):2146-60. doi: 10.1002/prot.23035. Epub 2011 May 2. PubMed

Godzik A. Metagenomics and the protein universe. Curr Opin Struct Biol. 2011 Jun;21(3):398-403. Epub 2011 Apr 14. Review. PubMed

Das D, Herve M, Feuerhelm J, Farr CL, Chiu HJ, Elsliger MA, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IA. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein. PLoS One. 2011 Mar 18;6(3):e17624. PubMed

Zmasek CM, Godzik A. Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol. 2011;12(1):R4. Epub 2011 Jan 17. PubMed

Stranzl GR, Santelli E, Bankston LA, La Clair C, Bobkov A, Schwarzenbacher R, Godzik A, Perego M, Grynberg M, Liddington RC. Structural insights into inhibition of Bacillus anthracis sporulation by a novel class of non-heme globin sensor domains. J Biol Chem. 2011 Mar 11;286(10):8448-58. Epub 2011 Jan 7. PubMed

Ellrott K, Zmasek CM, Weekes D, Sri Krishna S, Bakolitsa C, Godzik A, Wooley J. TOPSAN: a dynamic web database for structural genomics. Nucleic Acids Res. 2011 Jan;39(Database issue):D494-6. Epub 2010 Oct 20. PubMed

2010    To Top

Pawlowski K, Muszewska A, Lenart A, Szczepinska T, Godzik A, Grynberg M. A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins. BMC Genomics. 2010 Oct 21;11:590. PubMed

Krishna SS, Weekes D, Bakolitsa C, Elsliger MA, Wilson IA, Godzik A, Wooley J. TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1143-7. Epub 2010 Sep 30. PubMed

Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wooley J, Wüthrich K, Wilson IA. The JCSG high-throughput structural biology pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1137-42. Epub 2010 Sep 30. PubMed

Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics. 2010 Dec 1;26(23):2983-5. Epub 2010 Oct 10. PubMed

Xu Q, Eguchi T, Mathews II, Rife CL, Chiu HJ, Farr CL, Feuerhelm J, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. J Mol Biol. 2010 Dec 3;404(3):403-17. Epub 2010 Oct 1. PubMed

Weekes D, Krishna SS, Bakolitsa C, Wilson IA, Godzik A, Wooley J. TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinformatics. 2010 Aug 17;11:426. PubMed

Ellrott K, Jaroszewski L, Li W, Wooley JC, Godzik A. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PLoS Comput Biol. 2010 Jun 3;6(6):e1000798. PubMed

Nakamura T, Cieplak P, Cho DH, Godzik A, Lipton SA. S-nitrosylation of Drp1 links excessive mitochondrial fission to neuronal injury in neurodegeneration. Mitochondrion. 2010 Aug;10(5):573-8. Epub 2010 May 4. Review. PubMed

Matsumoto Y, Xu Q, Miyazaki S, Kaito C, Farr CL, Axelrod HL, Chiu HJ, Klock HE, Knuth MW, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Sekimizu K, Wilson IA. Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module. Structure. 2010 Mar 14;18(4):537-47. PubMed

Zhang Q, Zmasek CM, Godzik A. Domain architecture evolution of pattern-recognition receptors. Immunogenetics. 2010 May;62(5):263-72. Epub 2010 Mar 2. PubMed

Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010 Feb 26;6(2):e1000667. Review. PubMed

2009    To Top

Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9. PubMed

Istomin AY, Godzik A. Understanding diversity of human innate immunity receptors: analysis of surface features of leucine-rich repeat domains in NLRs and TLRs. BMC Immunol. 2009 Sep 3;10:48. PubMed

Burra PV, Zhang Y, Godzik A, Stec B. Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10505-10. Epub 2009 Jun 24. Erratum in: Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12560. PubMed

Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C. PSI-2: structural genomics to cover protein domain family space. Structure. 2009 Jun 10;17(6):869-81. Review. PubMed

An Y, Chen CY, Moyer B, Rotkiewicz P, Elsliger MA, Godzik A, Wilson IA, Balch WE. Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering. J Mol Biol. 2009 Aug 7;391(1):26-41. Epub 2009 May 4. PubMed

Grynberg M, Godzik A. The signal for signaling, found. PLoS Pathog. 2009 Apr;5(4):e1000398. Epub 2009 Apr 24. PubMed

Cho DH, Nakamura T, Fang J, Cieplak P, Godzik A, Gu Z, Lipton SA. S-nitrosylation of Drp1 mediates beta-amyloid-related mitochondrial fission and neuronal injury. Science. 2009 Apr 3;324(5923):102-5. PubMed

Xu Q, Sudek S, McMullan D, Miller MD, Geierstanger B, Jones DH, Krishna SS,Spraggon G, Bursalay B, Abdubek P, Acosta C, Ambing E, Astakhova T, Axelrod HL,Carlton D, Caruthers J, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Won Han G, Haugen J, Jaroszewski L, JinKK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Nigoghossian E,Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Trout CV, van den Bedem H,Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-DiaminoAcid Endopeptidase. Structure. 2009 Feb 13;17(2):303-313.   PubMed

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, BurleySK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A,Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T,Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a Workshop on Applications of Protein Models in Biomedical Research. Structure. 2009 Feb 13;17(2):151-159.   PubMed

Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B. Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics. 2009 Feb 5. [Epub ahead of print]   PubMed

Xu Q, McMullan D, Abdubek P, Astakhova T, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Hale J, Han GW,Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Sri Krishna S, Kumar A, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L,Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Trame C, van denBedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, WilsonIA. A structural basis for the regulatory inactivation of DnaA. J Mol Biol. 2009 Jan 16;385(2):368-80. Epub 2008 Oct 30.   PubMed

Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J,Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009 Feb;3(2):179-89. Epub 2008 Oct 30.   PubMed

Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K,Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 2009 Jan;37(Database issue):D611-8. Epub 2008 Oct 8.   PubMed

2008    to top

Jaroszewski L, Slabinski L, Wooley J, Deacon AM, Lesley SA, Wilson IA, Godzik A. Genome pool strategy for structural coverage of protein families. Structure. 2008 Nov 12;16(11):1659-67.   PubMed

Li W, Wooley JC, Godzik A. Probing metagenomics by rapid cluster analysis of very large datasets. PLoS ONE. 2008;3(10):e3375. Epub 2008 Oct 10.   PubMed

Veeramalai M, Ye Y, Godzik A. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics. 2008 Aug 31;9(1):35

Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, Godzik A. Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biol. 2008 Aug 4;9(8):R123.    PubMed

Holland LZ, Albalat R, Azumi K, Benito-Gutierrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernandez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008 Jul;18(7):1100-11. Epub 2008 Jun 18.    PubMed

Le Negrate G, Krieg A, Faustin B, Loeffler M, Godzik A, Krajewski S, Reed JC. ChlaDub1 of Chlamydia trachomatis suppresses NF-kappaB activation and inhibits IkappaBalpha ubiquitination and degradation. Cell Microbiol. 2008 Jun 16.    PubMed

Le Negrate G, Faustin B, Welsh K, Loeffler M, Krajewska M, Hasegawa P, Mukherjee S, Orth K, Krajewski S, Godzik A, Guiney DG, Reed JC. Salmonella secreted factor L deubiquitinase of Salmonella typhimurium inhibits NF-kappaB, suppresses IkappaBalpha ubiquitination and modulates innate immune responses.. J Immunol. 2008 Apr 1;180(7):5045-56.    PubMed

Ting JP, Lovering RC, Alnemri ES, Bertin J, Boss JM, Davis BK, Flavell RA, Girardin SE, Godzik A, Harton JA, Hoffman HM, Hugot JP, Inohara N, Mackenzie A, Maltais LJ, Nunez G, Ogura Y, Otten LA, Philpott D, Reed JC, Reith W, Schreiber S, Steimle V, Ward PA. The NLR gene family: a standard nomenclature. Immunity. 2008 Mar;28(3):285-7.    PubMed

Schwarzenbacher R, Godzik A, Jaroszewski L. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):133-40. Epub 2007 Dec 5.    PubMed

Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A. XtalPred: a web server for prediction of protein crystallizability. Bioinformatics. 2007 Dec 15;23(24):3403-5. Epub 2007 Oct 5.   PubMed

2007     to top

Zmasek CM, Zhang Q, Ye Y, Godzik A. Surprising complexity of the ancestral apoptosis network. Genome Biol. 2007 Oct 24;8(10):R226 [Epub ahead of print]   PubMed

Slabinski L, Jaroszewski L, Rodrigues AP, Rychlewski L, Wilson IA, Lesley SA, Godzik A. The challenge of protein structure determination--lessons from structuralgenomics. Protein Sci. 2007 Nov;16(11):2472-82.   PubMed

Zhang Y, Stec B, Godzik A. Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins. Structure. 2007 Sep;15(9):1141-7.   PubMed

Grynberg M, Li Z, Szczurek E, Godzik A. Putative type IV secretion genes in Bacillus anthracis. Trends Microbiol. 2007 May;15(5):191-5. Epub 2007 Mar 26.   PubMed

Friedberg I, Nika K, Tautz L, Saito K, Cerignoli F, Friedberg I, Godzik A,Mustelin T. Identification and characterization of DUSP27, a novel dual-specific proteinphosphatase. FEBS Lett. 2007 May 29;581(13):2527-33. Epub 2007 Apr 30.   PubMed

Rodrigues AP, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC Bioinformatics. 2007 May 22;8 Suppl 4:S1-4.    PubMed

Friedberg I, Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure. 2007 Apr;15(4):405-15.   PubMed

Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A. Using an alignment of fragment strings for comparing protein structures. Bioinformatics. 2007 Jan 15;23(2):e219-24.    PubMed

Sasin JM, Godzik A, Bujnicki JM. SURF'S UP! - protein classification by surface comparisons. J Biosci. 2007 Jan;32(1):97-100.   PubMed

Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW,Osterman AL, Godzik A. CutDB: a proteolytic event database. Nucleic Acids Res. 2007 Jan;35(Database issue):D546-9. Epub 2006 Nov 16.    PubMed

Awobuluyi M, Yang J, Ye Y, Chatterton JE, Godzik A, Lipton SA, Zhang D. Subunit-specific roles of glycine-binding domains in activation of NR1/NR3N-methyl-D-aspartate receptors. Mol Pharmacol. 2007 Jan;71(1):112-22. Epub 2006 Oct 17.   PubMed

Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H,Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y,Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A,Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe ofprotein families. PLoS Biol. 2007 Mar;5(3):e16.   PubMed

2006     to top

Friedberg I, Harder T, Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W379-81.    PubMed

Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci. 2006 Jun;15(6):1527-9.    PubMed

Li Z, Ye Y, Godzik A. Flexible Structural Neighborhood--a database of protein structural similarities and alignments. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D277-80.    PubMed

Ye Y, Li Z, and Godzik A. Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins Pacific Symposium on Biocomputing 11:439-450(2006) [PDF]

Li W, Godzik A. cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 May 26;    PubMed

Doukhanina EV, Chen S, van der Zalm E, Godzik A, Reed J, Dickman MB. Identification and functional characterization of the BAG protein family in Arabidopsis thaliana. J Biol Chem. 2006 Apr 24;    PubMed

Li W, Godzik A. VISSA: a program to visualize structural features from structure sequence alignment. Bioinformatics. 2006 Apr 1;22(7):887-8. Epub 2006 Jan 24.    PubMed

Robinson-Rechavi M, Alibes A, Godzik A. Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol. 2006 Feb 17;356(2):547-57. Epub 2005 Dec 7.    PubMed

Newman RM, Salunkhe P, Godzik A, Reed JC. Identification and characterization of a novel bacterial virulence factor that shares homology with mammalian Toll/interleukin-1 receptor family proteins. Infect Immun. 2006 Jan;74(1):594-601.    PubMed

Plewczynski D, Tkacz A, Wyrwicz LS, Godzik A, Kloczkowski A, Rychlewski L. Support-vector-machine classification of linear functional motifs in proteins. J Mol Model (Online). 2006 Aug;12(4):453-61. Epub 2005 Dec 10.    PubMed

Shiryaev SA, Ratnikov BI, Chekanov AV, Sikora S, Rozanov DV, Godzik A, Wang J, Smith JW, Huang Z, Lindberg I, Samuel MA, Diamond MS, Strongin AY. Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase. Biochem J. 2006 Jan 15;393(Pt 2):503-11.    PubMed

Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. Representing and comparing protein structures as paths in three-dimensionalspace. BMC Bioinformatics. 2006 Oct 20;7:460.    PubMed

Ginalski K, Godzik A, Rychlewski L. Novel SARS unique AdoMet-dependent methyltransferase. Cell Cycle. 2006 Oct;5(20):2414-6. Epub 2006 Oct 16.    PubMed

White AK, Hoch JA, Grynberg M, Godzik A, Perego M. Sensor domains encoded in Bacillus anthracis virulence plasmids preventsporulation by hijacking a sporulation sensor histidine kinase. J Bacteriol. 2006 Sep;188(17):6354-60.    PubMed

Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH,Dunbrack RL Jr, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, HeymannB, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B,Saibil H, Schwede T, Standley DM, Westbrook JD. Outcome of a workshop on archiving structural models of biologicalmacromolecules. Structure. 2006 Aug;14(8):1211-7.    PubMed

Doukhanina EV, Chen S, van der Zalm E, Godzik A, Reed J, Dickman MB. Identification and functional characterization of the BAG protein family inArabidopsis thaliana. Biol Chem. 2006 Jul 7;281(27):18793-801. Epub 2006 Apr 24.    PubMed

2005     to top

Friedberg I. and Godzik A. Connecting the Protein Structure Universe by Using Sparse Recurring Fragments. Structure (Camb.) (2005) Aug;13(8):1213-24 PubMed

Robinson-Rechavi M, Godzik A. Structural Genomics of Thermotoga maritima Proteins Shows that Contact Order Is a Major Determinant of Protein Thermostability. Structure (Camb). 2005 Jun;13(6):857-60. PubMed

Ye Y, Osterman A, Overbeek R, Godzik A. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics. 2005 Jun 1;21 Suppl 1:i478-i486. PubMed

Friedberg I, Godzik A. Fragnostic: walking through protein structure space. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W249-51. PubMed

Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8. PubMed

Plewczynski D, Tkacz A, Godzik A, Rychlewski L. A support vector machine approach to the identification of phosphorylation sites. Cell Mol Biol Lett. 2005;10(1):73-89. PubMed

Ginalski K, Grishin NV, Godzik A, Rychlewski L. Practical lessons from protein structure prediction. Nucleic Acids Res. 2005 Apr 1;33(6):1874-91. PubMed

Ye Y, Godzik A. Multiple flexible structure alignment using partial order graphs. Bioinformatics. 2005 Mar 3; PubMed

2004     to top

Friedberg I, Jaroszewski L, Ye Y, Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol. 2004 Jun;14(3):307-12. PubMed

Ye Y, Godzik A. Comparative analysis of protein domain organization. Genome Res. 2004 Mar;14(3):343-53. PubMed

Ye Y, Godzik A. Database searching by flexible protein structure alignment. Protein Sci. 2004 Jul;13(7):1841-50. PubMed

Sikora S, Godzik A. Combination of multiple alignment analysis and surface mapping paves a way for a detailed pathway reconstruction--the case of VHL (von Hippel-Lindau) protein and angiogenesis regulatory pathway. Protein Sci. 2004 Mar;13(3):786-96. Epub 2004 Feb 06. PubMed

Ye Y, Godzik A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W582-5. PubMed

Plewczynski D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A. Integrated web service for improving alignment quality based on segments comparison. BMC Bioinformatics. 2004 Jul 22;5(1):98. PubMed

Reed JC, Doctor KS, Godzik A. The domains of apoptosis: a genomics perspective. Sci STKE. 2004 Jun 22;2004(239):re9. Review. PubMed

Grynberg M, Godzik A. NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1. Trends Biochem Sci. 2004 Mar;29(3):106-10. PubMed

Ma H, Xiong H, Liu T, Zhang L, Godzik A, Zhang Z. Aggregate formation and synaptic abnormality induced by DSCR1. J Neurochem. 2004 Mar;88(6):1485-96. PubMed

Bourne PE, Allerston CK, Krebs W, Li W, Shindyalov IN, Godzik A, Friedberg I, Liu T, Wild D, Hwang S, Ghahramani Z, Chen L, Westbrook J. The status of structural genomics defined through the analysis of current targets and structures. Pac Symp Biocomput. 2004;:375-86. PubMed

Rozanov DV, Sikora S, Godzik A, Postnova TI, Golubkov V, Savinov A, Tomlinson S, Strongin AY. Non-proteolytic, Receptor/Ligand Interactions Associate Cellular Membrane Type-1 Matrix Metalloproteinase with the Complement Component C1q. J Biol Chem. 2004 Nov 26;279(48):50321-8. Epub 2004 Sep 16. PubMed

Alonso A, Burkhalter S, Sasin J, Tautz L, Bogetz J, Huynh H, Bremer MC, Holsinger LJ, Godzik A, Mustelin T. The minimal essential core of a cysteine-based protein-tyrosine phosphatase revealed by a novel 16-kDa VH1-like phosphatase, VHZ. J Biol Chem. 2004 Aug 20;279(34):35768-74. Epub 2004 Jun 16. PubMed

Alonso A, Sasin J, Bottini N, Friedberg I, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, Mustelin T. Protein tyrosine phosphatases in the human genome. Cell. 2004 Jun 11;117(6):699-711. Review. PubMed

Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L. The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1229-36. Epub 2004 Jun 22. PubMed

2003     to top

Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003 Oct;19 Suppl 2:II246-II255. PubMed

Godzik A. Fold recognition methods. Methods Biochem Anal. 2003;44:525-46. Review. PubMed

Ye Y, Jaroszewski L, Li W, Godzik A. A segment alignment approach to protein comparison. Bioinformatics. 2003 Apr 12;19(6):742-9. PubMed

Liu T, Rojas A, Ye Y, Godzik A. Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. Protein Sci. 2003 Sep;12(9):1872-81. PubMed

Grynberg M, Jaroszewski L, Godzik A. Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinformatics. 2003 Oct 10;4(1):46. PubMed

Grynberg M, Erlandsen H, Godzik A. HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins. Trends Biochem Sci. 2003 May;28(5):224-6. Review. PubMed

Alonso A, Rahmouni S, Williams S, van Stipdonk M, Jaroszewski L, Godzik A, Abraham RT, Schoenberger SP, Mustelin T. Tyrosine phosphorylation of VHR phosphatase by ZAP-70. Nat Immunol. 2003 Jan;4(1):44-8. Epub 2002 Nov 25. PubMed

Huynh H, Wang X, Li W, Bottini N, Williams S, Nika K, Ishihara H, Godzik A, Mustelin T. Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells. J Immunol. 2003 Dec 15;171(12):6661-71. PubMed

Chae HJ, Ke N, Kim HR, Chen S, Godzik A, Dickman M, Reed JC. Evolutionarily conserved cytoprotection provided by Bax Inhibitor-1 homologs from animals, plants, and yeast. Gene. 2003 Dec 24;323:101-13. PubMed

Bossy-Wetzel E, Barsoum MJ, Godzik A, Schwarzenbacher R, Lipton SA. Mitochondrial fission in apoptosis, neurodegeneration and aging. Curr Opin Cell Biol. 2003 Dec;15(6):706-16. Review. PubMed

Zhai D, Ke N, Zhang H, Ladror U, Joseph M, Eichinger A, Godzik A, Ng SC, Reed JC. Characterization of the anti-apoptotic mechanism of Bcl-B. Biochem J. 2003 Nov 15;376(Pt 1):229-36. PubMed

Reed JC, Doctor K, Rojas A, Zapata JM, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Godzik A; RIKEN GER Group; GSL Members. Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res. 2003 Jun;13(6B):1376-88. PubMed

Stehlik C, Hayashi H, Pio F, Godzik A, Reed JC. CARD6 is a modulator of NF-kappa B activation by Nod1- and Cardiak-mediated pathways. J Biol Chem. 2003 Aug 22;278(34):31941-9. Epub 2003 May 29. PubMed

Doctor KS, Reed JC, Godzik A, Bourne PE. The apoptosis database. Cell Death Differ. 2003 Jun;10(6):621-33. Review. PubMed

Luz JG, Hassig CA, Pickle C, Godzik A, Meyer BJ, Wilson IA. XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. Genes Dev. 2003 Apr 15;17(8):977-90. Epub 2003 Apr 02. PubMed

Stehlik C, Krajewska M, Welsh K, Krajewski S, Godzik A, Reed JC. The PAAD/PYRIN-only protein POP1/ASC2 is a modulator of ASC-mediated nuclear-factor-kappa B and pro-caspase-1 regulation. Biochem J. 2003 Jul 1;373(Pt 1):101-13. PubMed

Zhao Y, Hong DH, Pawlyk B, Yue G, Adamian M, Grynberg M, Godzik A, Li T. The retinitis pigmentosa GTPase regulator (RPGR)- interacting protein: subserving RPGR function and participating in disk morphogenesis. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3965-70. Epub 2003 Mar 21. PubMed

Chen EI, Li W, Godzik A, Howard EW, Smith JW. A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9. J Biol Chem. 2003 May 9;278(19):17158-63. Epub 2003 Feb 18. PubMed

2002     to top

Li W, Jaroszewski L, Godzik A. Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 2002 Aug;15(8):643-9. PubMed

Li W, Godzik A. Discovering new genes with advanced homology detection. Trends Biotechnol. 2002 Aug;20(8):315-6. PubMed

Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002 Jan;18(1):77-82. PubMed

Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci. 2002 Jul;11(7):1702-13. PubMed

Lipton SA, Choi YB, Takahashi H, Zhang D, Li W, Godzik A, Bankston LA. Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation. Trends Neurosci. 2002 Sep;25(9):474-80. Review. PubMed

Wu X, Li W, Sharma V, Godzik A, Freeze HH. Cloning and characterization of glucose transporter 11, a novel sugar transporter that is alternatively spliced in various tissues. Mol Genet Metab. 2002 May;76(1):37-45. PubMed

Fiorentino L, Stehlik C, Oliveira V, Ariza ME, Godzik A, Reed JC. A novel PAAD-containing protein that modulates NF-kappa B induction by cytokines tumor necrosis factor-alpha and interleukin-1beta. J Biol Chem. 2002 Sep 20;277(38):35333-40. Epub 2002 Jul 01. PubMed

Kridel SJ, Sawai H, Ratnikov BI, Chen EI, Li W, Godzik A, Strongin AY, Smith JW. A unique substrate binding mode discriminates membrane type-1 matrix metalloproteinase from other matrix metalloproteinases. J Biol Chem. 2002 Jun 28;277(26):23788-93. Epub 2002 Apr 16. PubMed

Stenner-Liewen F, Liewen H, Zapata JM, Pawlowski K, Godzik A, Reed JC. CADD, a Chlamydia protein that interacts with death receptors. J Biol Chem. 2002 Mar 22;277(12):9633-6. Epub 2002 Jan 22. PubMed

Alonso A, Merlo JJ, Na S, Kholod N, Jaroszewski L, Kharitonenkov A, Williams S, Godzik A, Posada JD, Mustelin T. Inhibition of T cell antigen receptor signaling by VHR-related MKPX (VHX), a new dual specificity phosphatase related to VH1 related (VHR). J Biol Chem. 2002 Feb 15;277(7):5524-8. Epub 2001 Dec 03. PubMed

Roth W, Stenner-Liewen F, Pawlowski K, Godzik A, Reed JC. Identification and characterization of DEDD2, a death effector domain-containing protein. J Biol Chem. 2002 Mar 1;277(9):7501-8. Epub 2001 Dec 11. PubMed

Chen EI, Kridel SJ, Howard EW, Li W, Godzik A, Smith JW. A unique substrate recognition profile for matrix metalloproteinase-2. J Biol Chem. 2002 Feb 8;277(6):4485-91. Epub 2001 Nov 02. PubMed

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R,Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C,Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A,Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A,Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5;420(6915):563-73. PubMed

Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11664-9. Epub 2002 Aug 22. PubMed

2001     to top

Pawlowski K, Rychlewski L, Zhang B, Godzik A. Fold predictions for bacterial genomes. J Struct Biol. 2001 May-Jun;134(2-3):219-31. Review. PubMed

Pawlowski K, Pio F, Chu Z, Reed JC, Godzik A. PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases. Trends Biochem Sci. 2001 Feb;26(2):85-7. PubMed

Pawlowski K, Godzik A. Surface map comparison: studying function diversity of homologous proteins. J Mol Biol. 2001 Jun 8;309(3):793-806. PubMed

Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 2001 Mar;17(3):282-3. PubMed

Damiano JS, Stehlik C, Pio F, Godzik A, Reed JC. CLAN, a novel human CED-4-like gene. Genomics. 2001 Jul;75(1-3):77-83. PubMed

Pathan N, Marusawa H, Krajewska M, Matsuzawa S, Kim H, Okada K, Torii S, Kitada S, Krajewski S, Welsh K, Pio F, Godzik A, Reed JC. TUCAN, an antiapoptotic caspase-associated recruitment domain family protein overexpressed in cancer. J Biol Chem. 2001 Aug 24;276(34):32220-9. Epub 2001 Jun 14. PubMed

Zapata JM, Pawlowski K, Haas E, Ware CF, Godzik A, Reed JC. A diverse family of proteins containing tumor necrosis factor receptor-associated factor domains. J Biol Chem. 2001 Jun 29;276(26):24242-52. Epub 2001 Feb 21. PubMed

Ke N, Godzik A, Reed JC. Bcl-B, a novel Bcl-2 family member that differentially binds and regulates Bax and Bak. J Biol Chem. 2001 Apr 20;276(16):12481-4. Epub 2001 Feb 21. PubMed

Chu ZL, Pio F, Xie Z, Welsh K, Krajewska M, Krajewski S, Godzik A, Reed JC. A novel enhancer of the Apaf1 apoptosome involved in cytochrome c-dependent caspase activation and apoptosis. J Biol Chem. 2001 Mar 23;276(12):9239-45. Epub 2000 Dec 11. PubMed

Guo B, Godzik A, Reed JC. Bcl-G, a novel pro-apoptotic member of the Bcl-2 family. J Biol Chem. 2001 Jan 26;276(4):2780-5. Epub 2000 Oct 27. PubMed

Marchenko GN, Ratnikov BI, Rozanov DV, Godzik A, Deryugina EI, Strongin AY. Characterization of matrix metalloproteinase-26, a novel metalloproteinase widely expressed in cancer cells of epithelial origin. Biochem J. 2001 Jun 15;356(Pt 3):705-18. PubMed

2000     to top

Jaroszewski L, Rychlewski L, Reed JC, Godzik A. ATP-activated oligomerization as a mechanism for apoptosis regulation: fold and mechanism prediction for CED-4. Proteins. 2000 May 15;39(3):197-203. PubMed

Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 2000 Feb;9(2):232-41. PubMed

Li W, Pio F, Pawlowski K, Godzik A. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics. 2000 Dec;16(12):1105-10. PubMed

Grynberg M, Topczewski J, Godzik A, Paszewski A. The Aspergillus nidulans cysA gene encodes a novel type of serine O-acetyltransferase which is homologous to homoserine O-acetyltransferases. Microbiology. 2000 Oct;146 ( Pt 10):2695-703. PubMed

Jaroszewski L, Godzik A. Search for a new description of protein topology and local structure. Proc Int Conf Intell Syst Mol Biol. 2000;8:211-7. PubMed

Jaroszewski L, Rychlewski L, Godzik A. Improving the quality of twilight-zone alignments. Protein Sci. 2000 Aug;9(8):1487-96. PubMed

Pawlowski K, Jaroszewski L, Rychlewski L, Godzik A. Sensitive sequence comparison as protein function predictor. Pac Symp Biocomput. 2000;:42-53. PubMed

Dunbrack RL Jr, Dunker K, Godzik A. Protein structure prediction in biology and medicine. Pac Symp Biocomput. 2000;(12):93-4. PubMed

Poole LB, Godzik A, Nayeem A, Schmitt JD. AhpF can be dissected into two functional units: tandem repeats of two thioredoxin-like folds in the N-terminus mediate electron transfer from the thioredoxin reductase-like C-terminus to AhpC. Biochemistry. 2000 Jun 6;39(22):6602-15. PubMed

Pawlowski K, Rychlewski L, Reed JC, Godzik A. From fold to function predictions: an apoptosis regulator protein BID. Comput Chem. 2000 May;24(3-4):511-7. PubMed

Zhang H, Huang Q, Ke N, Matsuyama S, Hammock B, Godzik A, Reed JC. Drosophila pro-apoptotic Bcl-2/Bax homologue reveals evolutionary conservation of cell death mechanisms. J Biol Chem. 2000 Sep 1;275(35):27303-6. PubMed

Zapata JM, Matsuzawa S, Godzik A, Leo E, Wasserman SA, Reed JC. The Drosophila tumor necrosis factor receptor-associated factor-1 (DTRAF1) interacts with Pelle and regulates NFkappaB activity. J Biol Chem. 2000 Apr 21;275(16):12102-7. PubMed

Zhang H, Xu Q, Krajewski S, Krajewska M, Xie Z, Fuess S, Kitada S, Pawlowski K, Godzik A, Reed JC. BAR: An apoptosis regulator at the intersection of caspases and Bcl-2 family proteins. Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2597-602. PubMed

1999     to top

Pawlowski K, Zhang B, Rychlewski L, Godzik A. The Helicobacter pylori genome: from sequence analysis to structural and functional predictions. Proteins. 1999 Jul 1;36(1):20-30. PubMed

Zhang B, Rychlewski L, Pawlowski K, Fetrow JS, Skolnick J, Godzik A. From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein Sci. 1999 May;8(5):1104-15. PubMed

Rychlewski L, Zhang B, Godzik A. Functional insights from structural predictions: analysis of the Escherichia coli genome. Protein Sci. 1999 Mar;8(3):614-24. PubMed

Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. 1999;Suppl 3:209-17. PubMed

Schendel SL, Azimov R, Pawlowski K, Godzik A, Kagan BL, Reed JC. Ion channel activity of the BH2 only Bcl-2 family member, BID. J Biol Chem. 1999 Jul 30;274(31):21932-6. PubMed

1998     to top

Rychlewski L, Zhang B, Godzik A. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des. 1998;3(4):229-38. PubMed

Fetrow JS, Godzik A. Function driven protein evolution. A possible proto-protein for the RNA-binding proteins. Pac Symp Biocomput. 1998;:485-96. PubMed

Jaroszewski L, Rychlewski L, Zhang B, Godzik A. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci. 1998 Jun;7(6):1431-40. PubMed

Zhang L, Godzik A, Skolnick J, Fetrow JS. Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Fold Des. 1998;3(6):535-48. PubMed

Fetrow JS, Godzik A, Skolnick J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. Mol Biol. 1998 Oct 2;282(4):703-11. PubMed

1997     to top

Rychlewski L, Godzik A. Secondary structure prediction using segment similarity. Protein Eng. 1997 Oct;10(10):1143-53. PubMed

Zhang B, Jaroszewski L, Rychlewski L, Godzik A. Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. Fold Des. 1997;2(5):307-17. PubMed

Pawlowski K, Jaroszewski L, Bierzynski A, Godzik A. Multiple model approach--dealing with alignment ambiguities in protein modeling. Pac Symp Biocomput. 1997;:328-39. PubMed

Hu WP, Godzik A, Skolnick J. Sequence-structure specificity--how does an inverse folding approach work? Protein Eng. 1997 Apr;10(4):317-31. PubMed

Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 1997 Mar;6(3):676-88. PubMed

Kolinski A, Skolnick J, Godzik A, Hu WP. A method for the prediction of surface "U"-turns and transglobular connections in small proteins. Proteins. 1997 Feb;27(2):290-308. PubMed

1996     to top

Kolinski A, Skolnick J, Godzik A. An algorithm for prediction of structural elements in small proteins. Pac Symp Biocomput. 1996;:446-60. PubMed

Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci. 1996 Jul;5(7):1325-38. PubMed

Pawlowski K, Bierzynski A, Godzik A. Structural diversity in a family of homologous proteins. J Mol Biol. 1996 May 3;258(2):349-66. PubMed

Godzik A. Knowledge-based potentials for protein folding: what can we learn from known protein structures? Structure. 1996 Apr 15;4(4):363-6. Review. PubMed

before 1995     to top

Godzik A, Kolinski A and Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of emergy parameter sets. Protein Sci. 1995 Oct;4(10):2107-17. PubMed

Godzik A. In search of the ideal protein sequence. Protein Eng. 1995 May;8(5):409-16. PubMed

Godzik A, Skolnick J. Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput Appl Biosci. 1994 Dec;10(6):587-96. PubMed

Godzik A, Kolinski A, Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol. 1992 Sep 5;227(1):227-38. PubMed

Godzik A, Skolnick J. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):12098-102. PubMed

Godzik A, Skolnick J, Kolinski A. Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins. Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2629-33. PubMed

Schweitzer ME, Brahme SK, Hodler J, Hanker GJ, Lynch TP, Flannigan BD, Godzik CA, Resnick D. Chronic wrist pain: spin-echo and short tau inversion recovery MR imaging and conventional and MR arthrography. Radiology. 1992 Jan;182(1):205-11. Erratum in: Radiology 1992 Aug;184(2):583. PubMed

Skolnick J, Kolinski A, Brooks CL 3rd, Godzik A, Rey A. A method for predicting protein structure from sequence. Curr Biol. 1993 Jul 1;3(7):414-23. PubMed

Godzik A, Skolnick J, Kolinski A. Regularities in interaction patterns of globular proteins. Protein Eng. 1993 Nov;6(8):801-10. PubMed

Godzik A, Kolinski A, Skolnick J. De novo and inverse folding predictions of protein structure and dynamics. J Comput Aided Mol Des. 1993 Aug;7(4):397-438. Review. PubMed

Skolnick J, Kolinski A, Godzik A. From independent modules to molten globules: observations on the nature of protein folding intermediates. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2099-100. Review. PubMed

Godzik A, Sander C. Conservation of residue interactions in a family of Ca-binding proteins. Protein Eng. 1989 Aug;2(8):589-96. PubMed

Godzik A, Boguta G, Wesolowski T. [Data bases in biochemistry--applications to analysis and prediction of protein properties and function] Postepy Biochem. 1989;35(1-2):45-61. Review. Polish. PubMed

Godzik A, Wesolowski T. On the interactions of charged side chains with the alpha-helix backbone. Biophys Chem. 1988 Aug;31(1-2):29-34. PubMed

Dadlez M, Bierzynski A, Godzik A, Sobocinska M, Kupryszewski G. Conformational role of His-12 in C-peptide of ribonuclease A. Biophys Chem. 1988 Aug;31(1-2):175-81. PubMed

Marszalek P, Godzik A. The Monte Carlo simulation of pearl chain formation. Radiat Environ Biophys. 1987;26(4):313-7. PubMed

Wesolowski TA, Godzik A, Geller M. Calculations of the conformational properties of acyclonucleosides. Part I. Stable conformations of acyclovir. Acta Biochim Pol. 1987;34(2):111-22. PubMed