메뉴 건너뛰기




Volumn 6, Issue , 2015, Pages

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYSUGAR; DEPSIPEPTIDE; GLYCOSYLATED PROTEIN; NATURAL PRODUCT; NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE; THANAMYCIN; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; BIOLOGICAL PRODUCT; LIPOPEPTIDE; PEPTIDE;

EID: 84942761231     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms9421     Document Type: Article
Times cited : (103)

References (68)
  • 1
    • 34247109045 scopus 로고    scopus 로고
    • Natural products as sources of new drugs over the last 25 years
    • Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. 70, 461-477 (2007).
    • (2007) J. Nat. Prod. , vol.70 , pp. 461-477
    • Newman, D.J.1    Cragg, G.M.2
  • 3
    • 42549160616 scopus 로고    scopus 로고
    • Nonribosomal peptide synthetases involved in the production of medically relevant natural products
    • Felnagle, E. A. et al. Nonribosomal peptide synthetases involved in the production of medically relevant natural products. Mol. Pharm. 5, 191-211 (2008).
    • (2008) Mol. Pharm. , vol.5 , pp. 191-211
    • Felnagle, E.A.1
  • 4
    • 69249202590 scopus 로고    scopus 로고
    • The biosynthetic logic of polyketide diversity
    • Hertweck, C. The biosynthetic logic of polyketide diversity. Angew. Chem. Int. Ed. 48, 4688-4716 (2009).
    • (2009) Angew. Chem. Int. Ed. , vol.48 , pp. 4688-4716
    • Hertweck, C.1
  • 5
    • 33748631825 scopus 로고    scopus 로고
    • Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms
    • Fischbach, M. A. & Walsh, C. T. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 106, 3468-3496 (2006).
    • (2006) Chem. Rev. , vol.106 , pp. 3468-3496
    • Fischbach, M.A.1    Walsh, C.T.2
  • 6
    • 0037046560 scopus 로고    scopus 로고
    • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    • Bentley, S. D. et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141-147 (2002).
    • (2002) Nature , vol.417 , pp. 141-147
    • Bentley, S.D.1
  • 7
    • 84861409243 scopus 로고    scopus 로고
    • Bacterial biosynthesis and maturation of the didemnin anti-cancer agents
    • Xu, Y. et al. Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. J. Am. Chem. Soc. 134, 8625-8632 (2012).
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 8625-8632
    • Xu, Y.1
  • 8
    • 85027943237 scopus 로고    scopus 로고
    • Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides
    • Freeman, M. F. et al. Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides. Science 338, 387-390 (2012).
    • (2012) Science , vol.338 , pp. 387-390
    • Freeman, M.F.1
  • 9
    • 67650436176 scopus 로고    scopus 로고
    • Drug discovery and natural products: End of an era or an endless frontier?
    • Li, J. W. & Vederas, J. C. Drug discovery and natural products: end of an era or an endless frontier? Science 325, 161-165 (2009).
    • (2009) Science , vol.325 , pp. 161-165
    • Li, J.W.1    Vederas, J.C.2
  • 10
    • 79959936207 scopus 로고    scopus 로고
    • NRPSpredictor2 - A web server for predicting NRPS adenylation domain specificity
    • Röttig, M. et al. NRPSpredictor2-a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39, W362-W367 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. W362-W367
    • Röttig, M.1
  • 11
    • 79959920872 scopus 로고    scopus 로고
    • AntiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
    • Medema, M. H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39, W339-W346 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. W339-W346
    • Medema, M.H.1
  • 12
    • 67650898253 scopus 로고    scopus 로고
    • Automated genome mining for natural products
    • Li, M. H. T. et al. Automated genome mining for natural products. BMC Bioinformatics 10, 185 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 185
    • Li, M.H.T.1
  • 13
    • 84876340080 scopus 로고    scopus 로고
    • Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models
    • Khayatt, B. I. et al. Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models. PloS ONE 8, e62136 (2013).
    • (2013) PloS ONE , vol.8 , pp. e62136
    • Khayatt, B.I.1
  • 14
    • 84856587901 scopus 로고    scopus 로고
    • NRPSsp: Non-ribosomal peptide synthase substrate predictor
    • Prieto, C. et al. NRPSsp: non-ribosomal peptide synthase substrate predictor. Bioinformatics 28, 426-427 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 426-427
    • Prieto, C.1
  • 15
    • 57149112966 scopus 로고    scopus 로고
    • ClustScan: An integrated program package for the semiautomatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures
    • Starcevic, A. et al. ClustScan: an integrated program package for the semiautomatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res. 36, 6882-6892 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6882-6892
    • Starcevic, A.1
  • 16
    • 84937761254 scopus 로고    scopus 로고
    • Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species
    • Duncan, K. R. et al. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chem. Biol. 22, 460-471 (2015).
    • (2015) Chem. Biol. , vol.22 , pp. 460-471
    • Duncan, K.R.1
  • 17
    • 84879908779 scopus 로고    scopus 로고
    • MS/MS networking guided analysis of molecule and gene cluster families
    • Nguyen, D. D. et al. MS/MS networking guided analysis of molecule and gene cluster families. Proc. Natl Acad. Sci. USA 110, E2611-E2620 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. E2611-E2620
    • Nguyen, D.D.1
  • 18
    • 84862999012 scopus 로고    scopus 로고
    • Mass spectral molecular networking of living microbial colonies
    • Watrous, J. et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl Acad. Sci. USA 109, E1743-E1752 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. E1743-E1752
    • Watrous, J.1
  • 19
    • 84885071517 scopus 로고    scopus 로고
    • Molecular networking as a dereplication strategy
    • Yang, J. Y. et al. Molecular networking as a dereplication strategy. J. Nat. Prod. 76, 1686-1699 (2013).
    • (2013) J. Nat. Prod. , vol.76 , pp. 1686-1699
    • Yang, J.Y.1
  • 20
    • 84907584619 scopus 로고    scopus 로고
    • Pep2Path: Automated mass spectrometry-guided genome mining of peptidic natural products
    • Medema, M. H. et al. Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products. PLoS Comput. Biol. 10, e1003822 (2014).
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003822
    • Medema, M.H.1
  • 21
    • 80054865417 scopus 로고    scopus 로고
    • A mass spectrometry-guided genome mining approach for natural product peptidogenomics
    • Kersten, R. D. et al. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 7, 794-802 (2011).
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 794-802
    • Kersten, R.D.1
  • 22
    • 84888095812 scopus 로고    scopus 로고
    • Glycogenomics as a mass spectrometry-guided genomemining method for microbial glycosylated molecules
    • Kersten, R. D. et al. Glycogenomics as a mass spectrometry-guided genomemining method for microbial glycosylated molecules. Proc. Natl Acad. Sci. USA 110, E4407-E4416 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. E4407-E4416
    • Kersten, R.D.1
  • 23
    • 84904554933 scopus 로고    scopus 로고
    • Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters
    • Cimermancic, P. et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421 (2014).
    • (2014) Cell , vol.158 , pp. 412-421
    • Cimermancic, P.1
  • 24
    • 84879938724 scopus 로고    scopus 로고
    • JSME: A free molecule editor in JavaScript
    • Bienfait, B. & Ertl, P. JSME: a free molecule editor in JavaScript. J. Cheminform. 5, 24 (2013).
    • (2013) J. Cheminform. , vol.5 , pp. 24
    • Bienfait, B.1    Ertl, P.2
  • 25
    • 34250656225 scopus 로고    scopus 로고
    • SmiLib v2. 0: A Java-based tool for rapid combinatorial library enumeration
    • Schüller, A., Ha?hnke, V. & Schneider, G. SmiLib v2. 0: a Java-based tool for rapid combinatorial library enumeration. QSAR Comb. Sci. 26, 407-410 (2007).
    • (2007) QSAR Comb. Sci , vol.26 , pp. 407-410
    • Schüller, A.1    Hahnke, V.2    Schneider, G.3
  • 26
    • 84869792678 scopus 로고    scopus 로고
    • Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery
    • Ibrahim, A. et al. Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery. Proc. Natl Acad. Sci. USA 109, 19196-19201 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 19196-19201
    • Ibrahim, A.1
  • 27
    • 34250710858 scopus 로고    scopus 로고
    • Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution
    • Rausch, C. et al. Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. BMC Evol. Biol. 7, 78 (2007).
    • (2007) BMC Evol. Biol. , vol.7 , pp. 78
    • Rausch, C.1
  • 28
    • 84868245096 scopus 로고    scopus 로고
    • New WS9326A congeners from Streptomyces sp. 9078 inhibiting Brugia malayi asparaginyl-tRNA synthetase
    • Yu, Z. et al. New WS9326A congeners from Streptomyces sp. 9078 inhibiting Brugia malayi asparaginyl-tRNA synthetase. Org. Lett. 14, 4946-4949 (2012).
    • (2012) Org. Lett. , vol.14 , pp. 4946-4949
    • Yu, Z.1
  • 29
    • 34848911303 scopus 로고    scopus 로고
    • Polyketide synthases and nonribosomal peptide synthetases: The emerging view from bacterial genomics
    • Donadio, S., Monciardini, P. & Sosio, M. Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat. Prod. Rep. 24, 1073-1109 (2007).
    • (2007) Nat. Prod. Rep. , vol.24 , pp. 1073-1109
    • Donadio, S.1    Monciardini, P.2    Sosio, M.3
  • 30
    • 84875476158 scopus 로고    scopus 로고
    • Gold biomineralization by a metallophore from a gold-associated microbe
    • Johnston, C. W. et al. Gold biomineralization by a metallophore from a gold-associated microbe. Nat. Chem. Biol. 9, 241-243 (2013).
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 241-243
    • Johnston, C.W.1
  • 31
    • 1842577641 scopus 로고    scopus 로고
    • Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria
    • Trivedi, O. A. et al. Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. Nature 428, 441-445 (2004).
    • (2004) Nature , vol.428 , pp. 441-445
    • Trivedi, O.A.1
  • 32
    • 84879944703 scopus 로고    scopus 로고
    • Bioinformatic evaluation of the secondary metabolism of antistaphylococcal environmental bacterial isolates
    • Wyatt, M. A. et al. Bioinformatic evaluation of the secondary metabolism of antistaphylococcal environmental bacterial isolates. Can. J. Microbiol. 59, 465-471 (2013).
    • (2013) Can. J. Microbiol. , vol.59 , pp. 465-471
    • Wyatt, M.A.1
  • 33
    • 0042844760 scopus 로고    scopus 로고
    • Antibiotic glycosyltransferases: Antibiotic maturation and prospects for reprogramming
    • Walsh, C., Freel-Meyers, C. L. & Losey, H. C. Antibiotic glycosyltransferases: antibiotic maturation and prospects for reprogramming. J. Med. Chem. 46, 3425-3436 (2003).
    • (2003) J. Med. Chem. , vol.46 , pp. 3425-3436
    • Walsh, C.1    Freel-Meyers, C.L.2    Losey, H.C.3
  • 34
    • 0032991245 scopus 로고    scopus 로고
    • Structural elucidation studies of erythromycins by electrospray tandem mass spectrometry
    • Gates, P. J. et al. Structural elucidation studies of erythromycins by electrospray tandem mass spectrometry. Rapid Commun. Mass Spectrom. 13, 242-246 (1999).
    • (1999) Rapid Commun. Mass Spectrom. , vol.13 , pp. 242-246
    • Gates, P.J.1
  • 35
    • 57549105096 scopus 로고    scopus 로고
    • Natural-product sugar biosynthesis and enzymatic glycodiversification
    • Thibodeaux, C. J., Melancon, 3rd C. E. & Liu, H. W. Natural-product sugar biosynthesis and enzymatic glycodiversification. Angew. Chem. Int. Ed. 47, 9814-9859 (2008).
    • (2008) Angew. Chem. Int. Ed. , vol.47 , pp. 9814-9859
    • Thibodeaux, C.J.1    Melancon, C.E.2    Liu, H.W.3
  • 36
    • 33746218306 scopus 로고    scopus 로고
    • Deciphering indolocarbazole and enediyne aminodideoxypentose biosynthesis through comparative genomics: Insights from the AT2433 biosynthetic locus
    • Gao, Q. et al. Deciphering indolocarbazole and enediyne aminodideoxypentose biosynthesis through comparative genomics: insights from the AT2433 biosynthetic locus. Chem. Biol. 13, 733-743 (2006).
    • (2006) Chem. Biol. , vol.13 , pp. 733-743
    • Gao, Q.1
  • 37
    • 0024419124 scopus 로고
    • Cloning of genes governing the deoxysugar portion of the erythromycin biosynthesis pathway in Saccharopolyspora erythraea (Streptomyces erythreus)
    • Vara, J. et al. Cloning of genes governing the deoxysugar portion of the erythromycin biosynthesis pathway in Saccharopolyspora erythraea (Streptomyces erythreus). J. Bacteriol. 171, 5872-5881 (1989).
    • (1989) J. Bacteriol. , vol.171 , pp. 5872-5881
    • Vara, J.1
  • 38
    • 5444249226 scopus 로고    scopus 로고
    • Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: Novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae
    • Ward, S. L. et al. Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae. Antimicrob. Agents Chemother. 48, 4703-4712 (2004).
    • (2004) Antimicrob. Agents Chemother. , vol.48 , pp. 4703-4712
    • Ward, S.L.1
  • 39
    • 0032514668 scopus 로고    scopus 로고
    • A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: Architecture of metabolic diversity
    • Xue, Y. et al. A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: architecture of metabolic diversity. Proc. Natl Acad. Sci. USA 95, 12111-12116 (1998).
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 12111-12116
    • Xue, Y.1
  • 40
    • 18444381437 scopus 로고    scopus 로고
    • NMR spectroscopy in the study of carbohydrates: Characterizing the structural complexity
    • Bubb, W. A. NMR spectroscopy in the study of carbohydrates: characterizing the structural complexity. Concept Magnetic Res. 19, 1-19 (2003).
    • (2003) Concept Magnetic Res. , vol.19 , pp. 1-19
    • Bubb, W.A.1
  • 41
    • 0017054958 scopus 로고
    • Biological glycosidation of macrolide aglycones. I. Isolation and characterization of 5-O-mycaminosyl narbonolide and 9-dihydro-5-O-mycaminosyl narbonolide
    • Maezawa, I., Kinumaki, A. & Suzuki, M. Biological glycosidation of macrolide aglycones. I. Isolation and characterization of 5-O-mycaminosyl narbonolide and 9-dihydro-5-O-mycaminosyl narbonolide. J. Antibiot. 29, 1203-1208 (1976).
    • (1976) J. Antibiot , vol.29 , pp. 1203-1208
    • Maezawa, I.1    Kinumaki, A.2    Suzuki, M.3
  • 42
    • 85031872088 scopus 로고
    • A new macrolide antibiotic kayamycin 10, 11-dihydro-5-0- mycaminosyl narbonolide produced by Nocardiopsis
    • Rengaraju et al. A new macrolide antibiotic kayamycin 10, 11-dihydro-5-0- mycaminosyl narbonolide produced by Nocardiopsis. Meiji Seika Kenkyu Nenpo 24, 52-54 (1985).
    • (1985) Meiji Seika Kenkyu Nenpo , vol.24 , pp. 52-54
    • Rengaraju1
  • 43
    • 79957595286 scopus 로고    scopus 로고
    • Deciphering the rhizosphere microbiome for diseasesuppressive bacteria
    • Mendes, R. et al. Deciphering the rhizosphere microbiome for diseasesuppressive bacteria. Science 332, 1097-1100 (2011).
    • (2011) Science , vol.332 , pp. 1097-1100
    • Mendes, R.1
  • 44
    • 84855301913 scopus 로고    scopus 로고
    • Cryptic polyketide synthase genes in nonpathogenic Clostridium SPP
    • Behnken, S. & Hertweck, C. Cryptic polyketide synthase genes in nonpathogenic Clostridium SPP. PloS ONE 7, e29609 (2012).
    • (2012) PloS ONE , vol.7 , pp. e29609
    • Behnken, S.1    Hertweck, C.2
  • 45
    • 84923349774 scopus 로고    scopus 로고
    • The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine
    • Cociancich, S. et al. The gyrase inhibitor albicidin consists of p-aminobenzoic acids and cyanoalanine. Nat. Chem. Biol. 11, 195-197 (2015).
    • (2015) Nat. Chem. Biol. , vol.11 , pp. 195-197
    • Cociancich, S.1
  • 46
    • 84874378581 scopus 로고    scopus 로고
    • Nonribosomal assembly of natural lipocyclocarbamate lipoprotein-associated phospholipase inhibitors
    • Johnston, C. W. et al. Nonribosomal assembly of natural lipocyclocarbamate lipoprotein-associated phospholipase inhibitors. ChemBioChem 14, 431-435 (2013).
    • (2013) ChemBioChem , vol.14 , pp. 431-435
    • Johnston, C.W.1
  • 47
    • 0035940857 scopus 로고    scopus 로고
    • Isolation structure determination, and phytotoxicity of unusual dioxopiperazines from the phytopathogenic fungus Phoma lingam
    • Pedras, M. S. & Biesenthal, C. J. Isolation, structure determination, and phytotoxicity of unusual dioxopiperazines from the phytopathogenic fungus Phoma lingam. Phytochemistry 58, 905-909 (2001).
    • (2001) Phytochemistry , vol.58 , pp. 905-909
    • Pedras, M.S.1    Biesenthal, C.J.2
  • 48
    • 0036203063 scopus 로고    scopus 로고
    • Involvement of a cytochrome P450 monooxygenase in thaxtomin A biosynthesis by Streptomyces acidiscabies
    • Healy, F. G. et al. Involvement of a cytochrome P450 monooxygenase in thaxtomin A biosynthesis by Streptomyces acidiscabies. J. Bacteriol. 184, 2019-2029 (2002).
    • (2002) J. Bacteriol. , vol.184 , pp. 2019-2029
    • Healy, F.G.1
  • 49
    • 79955040585 scopus 로고    scopus 로고
    • Biosynthetic gene cluster of the non-ribosomally synthesized cyclodepsipeptide skyllamycin: Deciphering unprecedented ways of unusual hydroxylation reactions
    • Pohle, S. et al. Biosynthetic gene cluster of the non-ribosomally synthesized cyclodepsipeptide skyllamycin: deciphering unprecedented ways of unusual hydroxylation reactions. J. Am. Chem. Soc. 133, 6194-6205 (2011).
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 6194-6205
    • Pohle, S.1
  • 50
    • 11144311139 scopus 로고    scopus 로고
    • Lessons from natural molecules
    • Clardy, J. & Walsh, C. T. Lessons from natural molecules. Nature 432, 829-837 (2004).
    • (2004) Nature , vol.432 , pp. 829-837
    • Clardy, J.1    Walsh, C.T.2
  • 51
    • 70350722394 scopus 로고    scopus 로고
    • Genomic basis for natural product biosynthetic diversity in the actinomycetes
    • Nett, M., Ikeda, H. & Moore, B. S. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat. Prod. Rep. 26, 1362-1384 (2009).
    • (2009) Nat. Prod. Rep. , vol.26 , pp. 1362-1384
    • Nett, M.1    Ikeda, H.2    Moore, B.S.3
  • 52
    • 77649305354 scopus 로고    scopus 로고
    • Natural products version 2.0: Connecting genes to molecules
    • Walsh, C. T. & Fischbach, M. A. Natural products version 2.0: connecting genes to molecules. J. Am. Chem. Soc. 132, 2469-2493 (2010).
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 2469-2493
    • Walsh, C.T.1    Fischbach, M.A.2
  • 53
    • 68349086897 scopus 로고    scopus 로고
    • Dereplication and de novo sequencing of nonribosomal peptides
    • Ng, J. et al. Dereplication and de novo sequencing of nonribosomal peptides. Nat. Methods 6, 596-599 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 596-599
    • Ng, J.1
  • 54
    • 84883353135 scopus 로고    scopus 로고
    • AntiSMASH 2.0 - A versatile platform for genome mining of secondary metabolite producers
    • Blin, K. et al. antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 41, W204-W212 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. W204-W212
    • Blin, K.1
  • 55
    • 84904547209 scopus 로고    scopus 로고
    • Automated genome mining of ribosomal peptide natural products
    • Mohimani, H. et al. Automated genome mining of ribosomal peptide natural products. ACS Chem. Biol. 9, 1545-1551 (2014).
    • (2014) ACS Chem. Biol. , vol.9 , pp. 1545-1551
    • Mohimani, H.1
  • 56
    • 84906678559 scopus 로고    scopus 로고
    • NRPquest: Coupling mass spectrometry and genome mining for nonribosomal peptide discovery
    • Mohimani, H. et al. NRPquest: coupling mass spectrometry and genome mining for nonribosomal peptide discovery. J. Nat. Prod. 77, 1902-1909 (2014).
    • (2014) J. Nat. Prod. , vol.77 , pp. 1902-1909
    • Mohimani, H.1
  • 57
    • 38649109810 scopus 로고    scopus 로고
    • Clustering millions of tandem mass spectra
    • Frank, A. M. et al. Clustering millions of tandem mass spectra. J. Proteome Res. 7, 113-122 (2008).
    • (2008) J. Proteome Res. , vol.7 , pp. 113-122
    • Frank, A.M.1
  • 58
    • 84906328199 scopus 로고    scopus 로고
    • Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS
    • Zhang, Q. et al. Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS. Proc. Natl Acad. Sci. USA 111, 12031-12036 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 12031-12036
    • Zhang, Q.1
  • 59
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 60
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • Delcher, A. L. et al. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673-679 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 673-679
    • Delcher, A.L.1
  • 61
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: Interactive sequence similarity searching
    • Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29-W37 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 62
    • 84891782659 scopus 로고    scopus 로고
    • Pfam: The protein families database
    • Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D222-D230
    • Finn, R.D.1
  • 63
    • 84862221167 scopus 로고    scopus 로고
    • SMART 7: Recent updates to the protein domain annotation resource
    • Letunic, I., Doerks, T. & Bork, P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 40, D302-D305 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. D302-D305
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 64
    • 58149287683 scopus 로고    scopus 로고
    • In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites
    • Ansari, M. Z. et al. In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites. BMC Bioinformatics 9, 454 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 454
    • Ansari, M.Z.1
  • 65
    • 84920866686 scopus 로고    scopus 로고
    • Automated identification of depsipeptide natural products by an informatic search algorithm
    • Skinnider, M., Johnston, C. W., Zvanych, R. & Magarvey, N. A. Automated identification of depsipeptide natural products by an informatic search algorithm. ChemBioChem. 16, 223-227 (2014).
    • (2014) ChemBioChem. , vol.16 , pp. 223-227
    • Skinnider, M.1    Johnston, C.W.2    Zvanych, R.3    Magarvey, N.A.4
  • 66
    • 84870472070 scopus 로고    scopus 로고
    • BioJava: An open-source framework for bioinformatics in 2012
    • Prlić, A. et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 28, 2693-2695 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 2693-2695
    • Prlić, A.1
  • 67
    • 0037361967 scopus 로고    scopus 로고
    • The chemistry development kit (CDK): An open-source Java library for chemo- and bioinformatics
    • Steinbeck, C. et al. The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci. 43, 493-500 (2003).
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 493-500
    • Steinbeck, C.1
  • 68
    • 1142306159 scopus 로고    scopus 로고
    • Biosynthetic gene cluster of the glycopeptide antibiotic teicoplanin: Characterization of two glycosyltransferases and the key acyltransferase
    • Li, T. L. et al. Biosynthetic gene cluster of the glycopeptide antibiotic teicoplanin: characterization of two glycosyltransferases and the key acyltransferase. Chem. Biol. 11, 107-119 (2004).
    • (2004) Chem. Biol. , vol.11 , pp. 107-119
    • Li, T.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.