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Volumn 304, Issue 3-4, 2014, Pages 230-235

In silico tools for the analysis of antibiotic biosynthetic pathways

Author keywords

Antibiotics; Bioinformatics; Database; Genome mining; Non ribsomal peptide synthetase; NRPS; Polyketide; Secondary metabolite

Indexed keywords

ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT;

EID: 84899651850     PISSN: 14384221     EISSN: 16180607     Source Type: Journal    
DOI: 10.1016/j.ijmm.2014.02.001     Document Type: Short Survey
Times cited : (72)

References (49)
  • 6
    • 3442896886 scopus 로고    scopus 로고
    • NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases
    • Ansari M.Z., Yadav G., Gokhale R.S., Mohanty D. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res. 2004, 32:W405-W413.
    • (2004) Nucleic Acids Res. , vol.32
    • Ansari, M.Z.1    Yadav, G.2    Gokhale, R.S.3    Mohanty, D.4
  • 7
    • 64249084052 scopus 로고    scopus 로고
    • Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data
    • Bachmann B.O., Ravel J. Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol. 2009, 458:181-217.
    • (2009) Methods Enzymol. , vol.458 , pp. 181-217
    • Bachmann, B.O.1    Ravel, J.2
  • 8
    • 84893481062 scopus 로고    scopus 로고
    • Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing
    • Baranasic D., Zucko J., Diminic J., Gacesa R., Long P.F., Cullum J., Hranueli D., Starcevic A. Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing. J. Ind. Microbiol. Biotechnol. 2014, 41:461-467.
    • (2014) J. Ind. Microbiol. Biotechnol. , vol.41 , pp. 461-467
    • Baranasic, D.1    Zucko, J.2    Diminic, J.3    Gacesa, R.4    Long, P.F.5    Cullum, J.6    Hranueli, D.7    Starcevic, A.8
  • 9
    • 14544294545 scopus 로고    scopus 로고
    • Bioactive microbial metabolites
    • Bérdy J. Bioactive microbial metabolites. J. Antibiot. (Tokyo) 2005, 58:1-26.
    • (2005) J. Antibiot. (Tokyo) , vol.58 , pp. 1-26
    • Bérdy, J.1
  • 13
    • 0034013269 scopus 로고    scopus 로고
    • Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains
    • Challis G.L., Ravel J., Townsend C.A. Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem. Biol. 2000, 7:211-224.
    • (2000) Chem. Biol. , vol.7 , pp. 211-224
    • Challis, G.L.1    Ravel, J.2    Townsend, C.A.3
  • 14
    • 84871826475 scopus 로고    scopus 로고
    • Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery
    • Condurso H.L., Bruner S.D. Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery. Nat. Prod. Rep. 2012, 29:1099-1110.
    • (2012) Nat. Prod. Rep. , vol.29 , pp. 1099-1110
    • Condurso, H.L.1    Bruner, S.D.2
  • 15
    • 84876566794 scopus 로고    scopus 로고
    • ClusterMine360: a database of microbial PKS/NRPS biosynthesis
    • Conway K.R., Boddy C.N. ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res. 2013, 41:D402-D407.
    • (2013) Nucleic Acids Res. , vol.41
    • Conway, K.R.1    Boddy, C.N.2
  • 19
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 20
    • 84934442432 scopus 로고    scopus 로고
    • Bioinformatics approaches and software for detection of secondary metabolic gene clusters
    • Fedorova N.D., Moktali V., Medema M.H. Bioinformatics approaches and software for detection of secondary metabolic gene clusters. Methods Mol. Biol. 2012, 944:23-45.
    • (2012) Methods Mol. Biol. , vol.944 , pp. 23-45
    • Fedorova, N.D.1    Moktali, V.2    Medema, M.H.3
  • 21
    • 69249202590 scopus 로고    scopus 로고
    • The biosynthetic logic of polyketide diversity
    • Hertweck C. The biosynthetic logic of polyketide diversity. Angew. Chem. Int. Ed. 2009, 48:4688-4716.
    • (2009) Angew. Chem. Int. Ed. , vol.48 , pp. 4688-4716
    • Hertweck, C.1
  • 23
    • 23144453475 scopus 로고    scopus 로고
    • SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites
    • Kamra P., Gokhale R.S., Mohanty D. SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. Nucleic Acids Res. 2005, 33:W220-W225.
    • (2005) Nucleic Acids Res. , vol.33
    • Kamra, P.1    Gokhale, R.S.2    Mohanty, D.3
  • 25
    • 84864566650 scopus 로고    scopus 로고
    • PKMiner: a database for exploring type II polyketide synthases
    • Kim J., Yi G.S. PKMiner: a database for exploring type II polyketide synthases. BMC Microbiol. 2012, 12:169.
    • (2012) BMC Microbiol. , vol.12 , pp. 169
    • Kim, J.1    Yi, G.S.2
  • 28
    • 0021323901 scopus 로고
    • Cloning and expression of antibiotic production genes
    • Martin J.F., Gil J.A. Cloning and expression of antibiotic production genes. Biotechnology. (N.Y.) 1984, 2:63-72.
    • (1984) Biotechnology. (N.Y.) , vol.2 , pp. 63-72
    • Martin, J.F.1    Gil, J.A.2
  • 30
    • 34247279292 scopus 로고    scopus 로고
    • Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes
    • Minowa Y., Araki M., Kanehisa M. Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J. Mol. Biol. 2007, 368:1500-1517.
    • (2007) J. Mol. Biol. , vol.368 , pp. 1500-1517
    • Minowa, Y.1    Araki, M.2    Kanehisa, M.3
  • 32
    • 26944502019 scopus 로고    scopus 로고
    • Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
    • Rausch C., Weber T., Kohlbacher O., Wohlleben W., Huson D.H. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res. 2005, 33:5799-5808.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 5799-5808
    • Rausch, C.1    Weber, T.2    Kohlbacher, O.3    Wohlleben, W.4    Huson, D.H.5
  • 34
    • 76749111595 scopus 로고    scopus 로고
    • Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families
    • Röttig M., Rausch C., Kohlbacher O. Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PLoS Comput. Biol. 2010, 6:e1000636.
    • (2010) PLoS Comput. Biol. , vol.6
    • Röttig, M.1    Rausch, C.2    Kohlbacher, O.3
  • 35
    • 0033179468 scopus 로고    scopus 로고
    • The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases
    • Stachelhaus T., Mootz H.D., Marahiel M.A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem. Biol. 1999, 6:493-505.
    • (1999) Chem. Biol. , vol.6 , pp. 493-505
    • Stachelhaus, T.1    Mootz, H.D.2    Marahiel, M.A.3
  • 38
    • 57149112966 scopus 로고    scopus 로고
    • ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures
    • Starcevic A., Zucko J., Simunkovic J., Long P.F., Cullum J., Hranueli D. ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res. 2008, 36:6882-6892.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6882-6892
    • Starcevic, A.1    Zucko, J.2    Simunkovic, J.3    Long, P.F.4    Cullum, J.5    Hranueli, D.6
  • 39
    • 35248844459 scopus 로고    scopus 로고
    • ASMPKS: an analysis system for modular polyketide synthases
    • Tae H., Kong E.B., Park K. ASMPKS: an analysis system for modular polyketide synthases. BMC Bioinformatics 2007, 8:327.
    • (2007) BMC Bioinformatics , vol.8 , pp. 327
    • Tae, H.1    Kong, E.B.2    Park, K.3
  • 40
    • 64549110333 scopus 로고    scopus 로고
    • Development of an analysis program of type I polyketide synthase gene clusters using homology search and profile hidden Markov model
    • Tae H., Sohng J.K., Park K. Development of an analysis program of type I polyketide synthase gene clusters using homology search and profile hidden Markov model. J. Microbiol. Biotechnol. 2009, 19:140-146.
    • (2009) J. Microbiol. Biotechnol. , vol.19 , pp. 140-146
    • Tae, H.1    Sohng, J.K.2    Park, K.3
  • 42
    • 84883572507 scopus 로고    scopus 로고
    • BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides
    • van Heel A.J., de Jong A., Montalban-Lopez M., Kok J., Kuipers O.P. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res. 2013, 41:W448-W453.
    • (2013) Nucleic Acids Res. , vol.41
    • van Heel, A.J.1    de Jong, A.2    Montalban-Lopez, M.3    Kok, J.4    Kuipers, O.P.5
  • 43
    • 84859051266 scopus 로고    scopus 로고
    • PKSIIIexplorer: TSVM approach for predicting Type III polyketide synthase proteins
    • Vijayan M., Chandrika S.K., Vasudevan S.E. PKSIIIexplorer: TSVM approach for predicting Type III polyketide synthase proteins. Bioinformation 2011, 6:125-127.
    • (2011) Bioinformation , vol.6 , pp. 125-127
    • Vijayan, M.1    Chandrika, S.K.2    Vasudevan, S.E.3
  • 44
    • 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. 2010, 132:2469-2493.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 2469-2493
    • Walsh, C.T.1    Fischbach, M.A.2
  • 45
    • 61649111711 scopus 로고    scopus 로고
    • CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters
    • Weber T., Rausch C., Lopez P., Hoof I., Gaykova V., Huson D.H., Wohlleben W. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J. Biotechnol. 2009, 140:13-17.
    • (2009) J. Biotechnol. , vol.140 , pp. 13-17
    • Weber, T.1    Rausch, C.2    Lopez, P.3    Hoof, I.4    Gaykova, V.5    Huson, D.H.6    Wohlleben, W.7
  • 46
    • 84887116869 scopus 로고    scopus 로고
    • Motif-based method for the genome-wide prediction of eukaryotic gene clusters
    • Springer Verlag Berlin, Heidelberg, A. Petrosino, P. Maddalena, P. Pala (Eds.)
    • Wolf T., Shelest V., Shelest E. Motif-based method for the genome-wide prediction of eukaryotic gene clusters. ICIAP 2013 Workshops, LNCS 2013, 389-398. Springer Verlag Berlin, Heidelberg. A. Petrosino, P. Maddalena, P. Pala (Eds.).
    • (2013) ICIAP 2013 Workshops, LNCS , pp. 389-398
    • Wolf, T.1    Shelest, V.2    Shelest, E.3
  • 47
    • 0037466331 scopus 로고    scopus 로고
    • Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases
    • Yadav G., Gokhale R.S., Mohanty D. Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J. Mol. Biol. 2003, 328:335-363.
    • (2003) J. Mol. Biol. , vol.328 , pp. 335-363
    • Yadav, G.1    Gokhale, R.S.2    Mohanty, D.3
  • 48
    • 0041620248 scopus 로고    scopus 로고
    • SEARCHPKS: a program for detection and analysis of polyketide synthase domains
    • Yadav G., Gokhale R.S., Mohanty D. SEARCHPKS: a program for detection and analysis of polyketide synthase domains. Nucleic Acids Res. 2003, 31:3654-3658.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3654-3658
    • Yadav, G.1    Gokhale, R.S.2    Mohanty, D.3
  • 49
    • 84859078407 scopus 로고    scopus 로고
    • The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity
    • Ziemert N., Podell S., Penn K., Badger J.H., Allen E., Jensen P.R. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS ONE 2012, 7:e34064.
    • (2012) PLoS ONE , vol.7
    • Ziemert, N.1    Podell, S.2    Penn, K.3    Badger, J.H.4    Allen, E.5    Jensen, P.R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.