Bioinformatics Tools for the Discovery of New Nonribosomal Peptides.
暂无分享,去创建一个
Tilmann Weber | Valérie Leclère | Maude Pupin | Philippe Jacques | T. Weber | M. Pupin | P. Jacques | V. Leclère
[1] Gitanjali Yadav,et al. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases , 2004, Nucleic Acids Res..
[2] Daniel H. Huson,et al. Dendroscope: An interactive viewer for large phylogenetic trees , 2007, BMC Bioinformatics.
[3] Christopher N. Boddy,et al. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides , 2014, Journal of Industrial Microbiology & Biotechnology.
[4] P. Brick,et al. Structural basis for the activation of phenylalanine in the non‐ribosomal biosynthesis of gramicidin S , 1997, The EMBO journal.
[5] Ammar Abdo,et al. A new fingerprint to predict nonribosomal peptides activity , 2012, Journal of Computer-Aided Molecular Design.
[6] María Martín,et al. Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..
[7] Gregory Kucherov,et al. NORINE: a database of nonribosomal peptides , 2007, Nucleic Acids Res..
[8] Jacques Ravel,et al. Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. , 2009, Methods in enzymology.
[9] Jurica Zucko,et al. Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing , 2013, Journal of Industrial Microbiology & Biotechnology.
[10] J. Zucko,et al. ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures , 2008, Nucleic acids research.
[11] Peter Man-Un Ung,et al. Automated genome mining for natural products , 2009, BMC Bioinformatics.
[12] M. Marahiel,et al. Learning from Nature's Drug Factories: Nonribosomal Synthesisof MacrocyclicPeptides , 2003, Journal of bacteriology.
[13] Matthew R. Pocock,et al. The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.
[14] Bernhard Schölkopf,et al. Estimating the Support of a High-Dimensional Distribution , 2001, Neural Computation.
[15] Minoru Kanehisa,et al. Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. , 2007, Journal of molecular biology.
[16] Tatiana A. Tatusova,et al. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..
[17] Kai Blin,et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..
[18] Tilmann Weber,et al. Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution , 2007, BMC Evolutionary Biology.
[19] Tilmann Weber,et al. In silico tools for the analysis of antibiotic biosynthetic pathways. , 2014, International journal of medical microbiology : IJMM.
[20] Kai Blin,et al. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..
[21] S. Salzberg,et al. Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.
[22] G. Challis,et al. Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. , 2000, Chemistry & biology.
[23] Gitanjali Yadav,et al. SBSPKS: structure based sequence analysis of polyketide synthases , 2010, Nucleic Acids Res..
[24] T. Stachelhaus,et al. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. , 1999, Chemistry & biology.
[25] Gregory Kucherov,et al. Diversity of Monomers in Nonribosomal Peptides: towards the Prediction of Origin and Biological Activity , 2010, Journal of bacteriology.
[26] Jeff H. Chang,et al. A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528 , 2009, BMC Genomics.
[27] Carlos Prieto,et al. NRPSsp: non-ribosomal peptide synthase substrate predictor , 2012, Bioinform..
[28] M. Devignes,et al. Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery , 2014, PloS one.
[29] Kim Rutherford,et al. Artemis: sequence visualization and annotation , 2000, Bioinform..
[30] A. Berti,et al. Identification of a Biosynthetic Gene Cluster and the Six Associated Lipopeptides Involved in Swarming Motility of Pseudomonas syringae pv. tomato DC3000 , 2007, Journal of bacteriology.
[31] Bartek Wilczynski,et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..
[32] Yanli Wang,et al. PubChem: Integrated Platform of Small Molecules and Biological Activities , 2008 .
[33] R. Breitling,et al. Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast , 2013, Molecular biology and evolution.
[34] Kai Blin,et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..
[35] J. Badger,et al. The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity , 2012, PloS one.
[36] Valérie Leclère,et al. Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing , 2015, Nucleic Acids Res..
[37] H. Berman,et al. The future of the Protein Data Bank. , 2013, Biopolymers.
[38] M. Schäfer,et al. New linear lipopeptides produced by Pseudomonas cichorii SF1-54 are involved in virulence, swarming motility, and biofilm formation. , 2013, Molecular plant-microbe interactions : MPMI.
[39] Tilmann Weber,et al. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs) , 2005, Nucleic acids research.
[40] Steven Salzberg,et al. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..
[41] Kai Blin,et al. NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity , 2011, Nucleic Acids Res..
[42] Marnix H Medema,et al. Bioinformatics approaches and software for detection of secondary metabolic gene clusters. , 2012, Methods in molecular biology.
[43] Gregory Kucherov,et al. Structural pattern matching of nonribosomal peptides , 2009, BMC Structural Biology.
[44] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..