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Papers authored by Godzik A

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Three-dimensional structural view of the central metabolic network of Thermotoga maritima.

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Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, and Godzik A

Science (New York, N.Y.) 325(5947):1544-9, 2009 Sep 18 - Who cited this? | PubMed ID: 19762644 | Fulltext

Structural and Functional Characterizations of SsgB, a Conserved Activator of Developmental Cell Division in Morphologically Complex Actinomycetes.

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Xu Q, Traag BA, Willemse J, McMullan D, Miller MD, Elsliger MA, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chruszcz M, Clayton T, Das D,

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The Journal of biological chemistry 284(37):25268-79, 2009 Sep 11 - Who cited this? | PubMed ID: 19567872 | Fulltext

Exploration of uncharted regions of the protein universe.

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Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, and Godzik A

PLoS biology 7(9):e1000205, 2009 Sep - Who cited this? | PubMed ID: 19787035 | Fulltext

Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering.

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An Y, Chen CY, Moyer B, Rotkiewicz P, Elsliger MA, Godzik A, Wilson IA, and Balch WE

Journal of molecular biology 391(1):26-41, 2009 Aug 7 - Who cited this? | PubMed ID: 19414022 | Fulltext

Crystal structure of histidine phosphotransfer protein ShpA, an essential regulator of stalk biogenesis in Caulobacter crescentus.

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Xu Q, Carlton D, Miller MD, Elsliger MA, Krishna SS, Abdubek P, Astakhova T, Burra P, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Feuerhelm J, Grant JC, Grzechnik A,

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Journal of molecular biology 390(4):686-98, 2009 Jul 24 - Who cited this? | PubMed ID: 19450606 | Fulltext

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure.

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Burra PV, Zhang Y, Godzik A, and Stec B

Proceedings of the National Academy of Sciences of the United States of America 106(26):10505-10, 2009 Jun 30 - Who cited this? | PubMed ID: 19553204 | Fulltext

PSI-2: Structural Genomics to Cover Protein Domain Family Space.

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Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, and Orengo C

Structure (London, England : 1993) 17(6):869-81, 2009 Jun 10 - Who cited this? | PubMed ID: 19523904 | Fulltext

Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

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Das D, Kozbial P, Axelrod HL, Miller MD, McMullan D, Krishna SS, Abdubek P, Acosta C, Astakhova T, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L,

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Proteins 75(2):296-307, 2009 May 1 - Who cited this? | PubMed ID: 19173316 | Fulltext

S-nitrosylation of Drp1 mediates beta-amyloid-related mitochondrial fission and neuronal injury.

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Cho DH, Nakamura T, Fang J, Cieplak P, Godzik A, Gu Z, and Lipton SA

Science (New York, N.Y.) 324(5923):102-5, 2009 Apr 3 - Who cited this? | PubMed ID: 19342591 | Fulltext

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution.

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Das D, Krishna SS, McMullan D, Miller MD, Xu Q, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y,

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Proteins 75(1):264-71, 2009 Apr - Who cited this? | PubMed ID: 19127588 | Fulltext

Structural genomics is the largest contributor of novel structural leverage.

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Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, and Rost B

Journal of structural and functional genomics 10(2):181-91, 2009 Apr - Who cited this? | PubMed ID: 19194785 | Fulltext

The signal for signaling, found.

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Grynberg M and Godzik A

PLoS pathogens 5(4):e1000398, 2009 Apr - Who cited this? | PubMed ID: 19390616 | Fulltext

Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.

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Xu Q, Rife CL, Carlton D, Miller MD, Krishna SS, Elsliger MA, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L,

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Proteins 74(4):1041-9, 2009 Mar - Who cited this? | PubMed ID: 19089981 | Fulltext

Outcome of a workshop on applications of protein models in biomedical research.

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Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C,

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Structure (London, England : 1993) 17(2):151-9, 2009 Feb 13 - Who cited this? | PubMed ID: 19217386 | Fulltext

Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.

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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,

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Structure (London, England : 1993) 17(2):303-13, 2009 Feb 13 - Who cited this? | PubMed ID: 19217401 | Fulltext

A structural basis for the regulatory inactivation of DnaA.

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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,

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Journal of molecular biology 385(2):368-80, 2009 Jan 16 - Who cited this? | PubMed ID: 19000695 | Fulltext

Understanding diversity of human innate immunity receptors: analysis of surface features of leucine-rich repeat domains in NLRs and TLRs.

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Istomin AY and Godzik A

BMC immunology 10:48, 2009 - Who cited this? | PubMed ID: 19728889 | Fulltext

Genome pool strategy for structural coverage of protein families.

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Jaroszewski L, Slabinski L, Wooley J, Deacon AM, Lesley SA, Wilson IA, and Godzik A

Structure (London, England : 1993) 16(11):1659-67, 2008 Nov - Who cited this? | PubMed ID: 19000818 | Fulltext

Shotgun metaproteomics of the human distal gut microbiota.

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Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, and Jansson JK

The ISME journal, 2008 Oct 30 - Who cited this? | PubMed ID: 18971961 | Fulltext

PMAP: databases for analyzing proteolytic events and pathways.

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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, and Eroshkin AM

Nucleic acids research, 2008 Oct 8 - Who cited this? | PubMed ID: 18842634 | Fulltext

ChlaDub1 of Chlamydia trachomatis suppresses NF-kappaB activation and inhibits IkappaBalpha ubiquitination and degradation.

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Le Negrate G, Krieg A, Faustin B, Loeffler M, Godzik A, Krajewski S, and Reed JC

Cellular microbiology 10(9):1879-92, 2008 Sep - Who cited this? | PubMed ID: 18503636 | Fulltext

TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.

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Veeramalai M, Ye Y, and Godzik A

BMC bioinformatics 9(1):358, 2008 Aug 31 - Who cited this? | PubMed ID: 18759993 | Fulltext

Novel genes dramatically alter regulatory network topology in amphioxus.

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Zhang Q, Zmasek CM, Dishaw LJ, Mueller MG, Ye Y, Litman GW, and Godzik A

Genome biology 9(8):R123, 2008 Aug 4 - Who cited this? | PubMed ID: 18680598 | Fulltext

The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

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Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F,

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Genome research, 2008 Jun 18 - Who cited this? | PubMed ID: 18562680 | Fulltext

Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold.

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Kozbial P, Xu Q, Chiu HJ, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Carlton D, Clayton T, Deller M, Duan L, Elias Y, Elsliger MA,

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Proteins 71(3):1589, 2008 May 15 - Who cited this? | PubMed ID: 18324683 | Fulltext

Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution.

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Xu Q, Kozbial P, McMullan D, Krishna SS, Brittain SM, Ficarro SB, DiDonato M, Miller MD, Abdubek P, Axelrod HL, Chiu HJ, Clayton T, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK,

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Proteins 71(3):1546, 2008 May 15 - Who cited this? | PubMed ID: 18275082 | Fulltext

Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution.

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Axelrod HL, McMullan D, Krishna SS, Miller MD, Elsliger MA, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW,

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Proteins 71(2):1042, 2008 May 1 - Who cited this? | PubMed ID: 18260100 | Fulltext

Salmonella secreted factor L deubiquitinase of Salmonella typhimurium inhibits NF-kappaB, suppresses IkappaBalpha ubiquitination and modulates innate immune responses.

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Le Negrate G, Faustin B, Welsh K, Loeffler M, Krajewska M, Hasegawa P, Mukherjee S, Orth K, Krajewski S, Godzik A, Guiney DG, and Reed JC

Journal of immunology (Baltimore, Md. : 1950) 180(7):5045, 2008 Apr 1 - Who cited this? | PubMed ID: 18354230 | Fulltext

The NLR gene family: a standard nomenclature.

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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,

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Immunity 28(3):285, 2008 Mar - Who cited this? | PubMed ID: 18341998 | Fulltext

Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.

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Mathews II, McMullan D, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K,

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Proteins 70(2):603, 2008 Feb 1 - Who cited this? | PubMed ID: 18004772 | Fulltext

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches.

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Schwarzenbacher R, Godzik A, and Jaroszewski L

Acta crystallographica. Section D, Biological crystallography 64(Pt 1):133, 2008 Jan - Who cited this? | PubMed ID: 18094477 | Fulltext

Probing metagenomics by rapid cluster analysis of very large datasets.

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Li W, Wooley JC, and Godzik A

PLoS ONE 3(10):e3375, 2008 - Who cited this? | PubMed ID: 18846219 | Fulltext

XtalPred: a web server for prediction of protein crystallizability.

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Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, and Godzik A

Bioinformatics (Oxford, England) 23(24):3403-5, 2007 Dec 15 - Who cited this? | PubMed ID: 17921170 | Fulltext

Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 A resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate.

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Xu Q, Saikatendu KS, Krishna SS, McMullan D, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J,

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Proteins 69(2):433, 2007 Nov 1 - Who cited this? | PubMed ID: 17654724 | Fulltext

Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.

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Zubieta C, Joseph R, Krishna SS, McMullan D, Kapoor M, Axelrod HL, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y,

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Proteins 69(2):234, 2007 Nov 1 - Who cited this? | PubMed ID: 17654547 | Fulltext

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.

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Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA,

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Proteins 69(2):223, 2007 Nov 1 - Who cited this? | PubMed ID: 17654545 | Fulltext

Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 A resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases.

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Krishna SS, Tautz L, Xu Q, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK,

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Proteins 69(2):415, 2007 Nov 1 - Who cited this? | PubMed ID: 17636569 | Fulltext

The challenge of protein structure determination--lessons from structural genomics.

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Slabinski L, Jaroszewski L, Rodrigues AP, Rychlewski L, Wilson IA, Lesley SA, and Godzik A

Protein science : a publication of the Protein Society 16(11):2472-82, 2007 Nov - Who cited this? | PubMed ID: 17962404 | Fulltext

Computational protein function prediction: are we making progress?.

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Godzik A, Jambon M, and Friedberg I

Cellular and molecular life sciences : CMLS 64(19-20):2505-11, 2007 Oct - Who cited this? | PubMed ID: 17611711 | Fulltext

Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution.

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Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA,

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Proteins 68(4):999, 2007 Sep 1 - Who cited this? | PubMed ID: 17546672 | Fulltext

Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins.

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Zhang Y, Stec B, and Godzik A

Structure (London, England : 1993) 15(9):1141-7, 2007 Sep - Who cited this? | PubMed ID: 17850753 | Fulltext

Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function.

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Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA,

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Proteins 68(1):418-24, 2007 Jul 1 - Who cited this? | PubMed ID: 17444523 | Fulltext

Identification and characterization of DUSP27, a novel dual-specific protein phosphatase.

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Friedberg I, Nika K, Tautz L, Saito K, Cerignoli F, Friedberg I, Godzik A, and Mustelin T

FEBS letters 581(13):2527-33, 2007 May 29 - Who cited this? | PubMed ID: 17498703 | Fulltext

Putative type IV secretion genes in Bacillus anthracis.

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Grynberg M, Li Z, Szczurek E, and Godzik A

Trends in microbiology 15(5):191-5, 2007 May - Who cited this? | PubMed ID: 17387016 | Fulltext

Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution.

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Weekes D, Miller MD, Krishna SS, McMullan D, McPhillips TM, Acosta C, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Morse AT,

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Proteins 67(1):247, 2007 Apr 1 - Who cited this? | PubMed ID: 17256761 | Fulltext

Functional differentiation of proteins: implications for structural genomics.

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Friedberg I and Godzik A

Structure (London, England : 1993) 15(4):405-15, 2007 Apr - Who cited this? | PubMed ID: 17437713 | Fulltext

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

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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,

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PLoS biology 5(3), 2007 Mar - Who cited this? | PubMed ID: 17355171 | Fulltext

Using an alignment of fragment strings for comparing protein structures.

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Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, and Godzik A

Bioinformatics (Oxford, England) 23(2):e219-24, 2007 Jan 15 - Who cited this? | PubMed ID: 17237095 | Fulltext

Surprising complexity of the ancestral apoptosis network.

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Zmasek CM, Zhang Q, Ye Y, and Godzik A

Genome biology 8(10), 2007 - Who cited this? | PubMed ID: 17958905 | Fulltext

CutDB: a proteolytic event database.

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Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, and Godzik A

Nucleic acids research 35(Database issue), 2007 Jan - Who cited this? | PubMed ID: 17142225 | Fulltext

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