SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria (Q38716880)

5 September 2017

SANDPUMA: Ensemble Predictions of Nonribosomal Peptide Chemistry Reveals Biosynthetic Diversity across Actinobacteria (English)

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5 September 2017

1

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1 June 2020

Marnix H Medema

series ordinal

5

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1 June 2020

3

Oliver Kohlbacher

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1 June 2020

4

Cameron R Currie

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author name string

Fabian Aicheler

series ordinal

2

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1 June 2020

language of work or name

English

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publication date

19 June 2017

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5 September 2017

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1 June 2020

volume

33

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issue

20

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1 June 2020

page(s)

3202-3210

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describes a project that uses

1 June 2020

Cytoscape

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9 June 2022

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based on heuristic

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cites work

Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Evolutionary concepts in natural products discovery: what actinomycetes have taught us.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

A roadmap for natural product discovery based on large-scale genomics and metabolomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Accelerated Profile HMM Searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Prodigal: prokaryotic gene recognition and translation initiation site identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Clustal W and Clustal X version 2.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Automated genome mining for natural products.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

An initial strategy for comparing proteins at the domain architecture level

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Clinical practice guidelines by the infectious diseases society of america for the treatment of methicillin-resistant Staphylococcus aureus infections in adults and children: executive summary

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Minimum Information about a Biosynthetic Gene cluster.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

FastTree 2--approximately maximum-likelihood trees for large alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

NRPSsp: non-ribosomal peptide synthase substrate predictor

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Recombination and selectional forces in cyanopeptolin NRPS operons from highly similar, but geographically remote Planktothrix strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

A hybrid polyketide-nonribosomal peptide in nematodes that promotes larval survival

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTX400

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Insights into the chemical logic and enzymatic machinery of NRPS assembly lines

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Fast and sensitive protein alignment using DIAMOND

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms.

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860034

10.1093/BIOINFORMATICS/BTX400

4 November 2018

Identifiers

DOI

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journals/bioinformatics/ChevretteAKCM17

1 June 2020

DBLP publication ID

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DBLP Dataset 2021-01-02

28 January 2021

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28633438%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

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