HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

[1]  L. Pearl,et al.  Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus , 2022, Nature Communications.

[2]  M. Medema,et al.  Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases , 2021, Nature Chemical Biology.

[3]  Alexander M. Kloosterman,et al.  antiSMASH 6.0: improving cluster detection and comparison capabilities , 2021, Nucleic Acids Res..

[4]  Elizabeth I. Parkinson,et al.  A community resource for paired genomic and metabolomic data mining , 2021, Nature Chemical Biology.

[5]  Chad W. Johnston,et al.  Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences , 2020, Nature Communications.

[6]  Benjamin A. Shoemaker,et al.  PubChem in 2021: new data content and improved web interfaces , 2020, Nucleic Acids Res..

[7]  Lutz Schmitt,et al.  New developments in RiPP discovery, enzymology and engineering. , 2020, Natural product reports.

[8]  A. Gurevich,et al.  MolDiscovery: learning mass spectrometry fragmentation of small molecules , 2020, Nature Communications.

[9]  A. Truman,et al.  Genome mining strategies for ribosomally synthesised and post-translationally modified peptides , 2020, Computational and structural biotechnology journal.

[10]  Douglas A. Mitchell,et al.  Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family , 2020, bioRxiv.

[11]  A. Sant’Ana,et al.  Natural products with preservative properties for enhancing the microbiological safety and extending the shelf-life of seafood: A review. , 2020, Food research international.

[12]  Chad W. Johnston,et al.  DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products , 2019, Proceedings of the National Academy of Sciences.

[13]  Mark F. Fisher,et al.  De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. , 2019, Cell systems.

[14]  Hosein Mohimani,et al.  MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. , 2019, Cell systems.

[15]  Justin J. J. van der Hooft,et al.  The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery , 2019, ACS central science.

[16]  Geoffrey I. Webb,et al.  DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites , 2019, Bioinform..

[17]  Graham A. Hudson,et al.  Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides. , 2019, Journal of the American Chemical Society.

[18]  Emmanuel L. C. de los Santos,et al.  NeuRiPP: Neural network identification of RiPP precursor peptides , 2019, Scientific Reports.

[19]  Andrew W Truman,et al.  Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool , 2018, bioRxiv.

[20]  J. Weng,et al.  Gene-guided discovery and engineering of branched cyclic peptides in plants , 2018, Proceedings of the National Academy of Sciences.

[21]  Liu Cao,et al.  Dereplication of microbial metabolites through database search of mass spectra , 2018, Nature Communications.

[22]  Oscar P. Kuipers,et al.  BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins , 2018, Nucleic Acids Res..

[23]  Hosein Mohimani,et al.  Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra , 2018, Nature Microbiology.

[24]  Debasisa Mohanty,et al.  RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links , 2017, Nucleic Acids Res..

[25]  Kai Blin,et al.  antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification , 2017, Nucleic Acids Res..

[26]  Christopher J. Schwalen,et al.  A new genome-mining tool redefines the lasso peptide biosynthetic landscape , 2016, Nature chemical biology.

[27]  I-Min A. Chen,et al.  IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes , 2016, Nucleic Acids Res..

[28]  Renzo Kottmann,et al.  The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters , 2016, Nucleic Acids Res..

[29]  Michael A. Skinnider,et al.  Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining , 2016, Proceedings of the National Academy of Sciences.

[30]  Joel S. Freundlich,et al.  Discovery of MRSA active antibiotics using primary sequence from the human microbiome , 2016, Nature chemical biology.

[31]  Kristian Fog Nielsen,et al.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.

[32]  Pieter C Dorrestein,et al.  Illuminating the dark matter in metabolomics , 2015, Proceedings of the National Academy of Sciences.

[33]  Maria F. Sassano,et al.  PRESTO-TANGO: an open-source resource for interrogation of the druggable human GPCR-ome , 2015, Nature Structural &Molecular Biology.

[34]  A. Harvey,et al.  The re-emergence of natural products for drug discovery in the genomics era , 2015, Nature Reviews Drug Discovery.

[35]  Rainer Breitling,et al.  Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products , 2014, PLoS Comput. Biol..

[36]  Huan Wang,et al.  Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS , 2014, Proceedings of the National Academy of Sciences.

[37]  Yota Otachi,et al.  Subgraph isomorphism in graph classes , 2012, Discret. Math..

[38]  Z. Deng,et al.  ThioFinder: A Web-Based Tool for the Identification of Thiopeptide Gene Clusters in DNA Sequences , 2012, PloS one.

[39]  Nuno Bandeira,et al.  Mass spectral molecular networking of living microbial colonies , 2012, Proceedings of the National Academy of Sciences.

[40]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[41]  David J Newman,et al.  Natural products as sources of new drugs over the 30 years from 1981 to 2010. , 2012, Journal of natural products.

[42]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[43]  Kai Blin,et al.  NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity , 2011, Nucleic Acids Res..

[44]  M. Bibb,et al.  Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides , 2010, Proceedings of the National Academy of Sciences.

[45]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[46]  G. Lomonossoff,et al.  pEAQ: versatile expression vectors for easy and quick transient expression of heterologous proteins in plants. , 2009, Plant biotechnology journal.

[47]  E. Dittmann,et al.  Ribosomal synthesis of tricyclic depsipeptides in bloom-forming cyanobacteria. , 2008, Angewandte Chemie.

[48]  J. Ravel,et al.  A global assembly line for cyanobactins. , 2008, Nature chemical biology.

[49]  Minoru Kanehisa,et al.  Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. , 2007, Journal of molecular biology.

[50]  J. McGivern.  Ziconotide: a review of its pharmacology and use in the treatment of pain , 2007, Neuropsychiatric disease and treatment.

[51]  J. M. Fernández-Abalos,et al.  Radamycin, a novel thiopeptide produced by streptomyces sp. RSP9. I. Taxonomy, fermentation, isolation and biological activities. , 2002, The Journal of antibiotics.

[52]  Clement Waine,et al.  Biosynthesis and insecticidal properties of plant cyclotides: The cyclic knotted proteins from Oldenlandia affinis , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[53]  G. Challis,et al.  Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. , 2000, FEMS microbiology letters.

[54]  A. Rincé,et al.  Characterization of the lacticin 481 operon: the Lactococcus lactis genes lctF, lctE, and lctG encode a putative ABC transporter involved in bacteriocin immunity , 1997, Applied and environmental microbiology.

[55]  A. Rincé,et al.  Cloning, expression, and nucleotide sequence of genes involved in production of lactococcin DR, a bacteriocin from lactococcus lactis subsp. lactis , 1994, Applied and environmental microbiology.

[56]  G. Jung,et al.  Epidermin: sequencing of a heterodetic tetracyclic 21-peptide amide antibiotic. , 1986, European journal of biochemistry.

[57]  Julian R. Ullmann,et al.  An Algorithm for Subgraph Isomorphism , 1976, J. ACM.

[58]  H. L. Morgan.  The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. , 1965 .

[59]  H. Komaki,et al.  Isolation and structure determination of a new thiopeptide globimycin from Streptomyces globisporus subsp. globisporus based on genome mining , 2018 .