The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. (Q47104996)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

title

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

1 reference

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

Hyun Uk Kim

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

author name string

Tilmann Weber

series ordinal

1

1 reference

http://europepmc.org/abstract/PMC/5640684

8 January 2018

Hyun Uk Kim

series ordinal

2

1 reference

http://europepmc.org/abstract/PMC/5640684

8 January 2018

publication date

5 February 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

Synthetic and systems biotechnology

8 April 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

volume

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

page(s)

69-79

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

StreptomeDB 2.0--an extended resource of natural products produced by streptomycetes

8 April 2020

cites work

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Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing.

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

23 May 2018

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ChEBI in 2016: Improved services and an expanding collection of metabolites

23 May 2018

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

23 May 2018

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A structural model for multimodular NRPS assembly lines

23 May 2018

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

23 May 2018

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23 May 2018

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23 May 2018

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Informatic search strategies to discover analogues and variants of natural product archetypes.

23 May 2018

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Metabolic profiling as a tool for prioritizing antimicrobial compounds

23 May 2018

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23 May 2018

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Minimum Information about a Biosynthetic Gene cluster.

23 May 2018

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Metabolomics in the natural products field--a gateway to novel antibiotics

23 May 2018

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IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites

23 May 2018

1 reference

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Motif-independent de novo detection of secondary metabolite gene clusters-toward identification from filamentous fungi

23 May 2018

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antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters

23 May 2018

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ChEMBL web services: streamlining access to drug discovery data and utilities

23 May 2018

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Reconstructing genome-scale metabolic models with merlin

23 May 2018

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CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

23 May 2018

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One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces

23 May 2018

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Global biogeographic sampling of bacterial secondary metabolism

23 May 2018

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Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes

23 May 2018

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Automated identification of depsipeptide natural products by an informatic search algorithm

23 May 2018

1 reference

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High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system.

23 May 2018

1 reference

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

23 May 2018

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

23 May 2018

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

23 May 2018

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

23 May 2018

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Structural rearrangements of a polyketide synthase module during its catalytic cycle

23 May 2018

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Structure of a modular polyketide synthase

23 May 2018

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23 May 2018

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Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: application to sequenced genomes of Aspergillus and ten other filamentous fungal species

23 May 2018

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Reprogramming acyl carrier protein interactions of an Acyl-CoA promiscuous trans-acyltransferase

23 May 2018

1 reference

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23 May 2018

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Improved lanthipeptide detection and prediction for antiSMASH

23 May 2018

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Chemical-biogeographic survey of secondary metabolism in soil

23 May 2018

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Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species

23 May 2018

1 reference

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MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data

23 May 2018

1 reference

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Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

23 May 2018

1 reference

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The ChEMBL bioactivity database: an update

23 May 2018

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Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides

23 May 2018

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Software platforms to facilitate reconstructing genome-scale metabolic networks

23 May 2018

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products

23 May 2018

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antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers

23 May 2018

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Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

23 May 2018

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BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides.

23 May 2018

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

23 May 2018

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The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum

23 May 2018

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Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

23 May 2018

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23 May 2018

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Natural products: a continuing source of novel drug leads

23 May 2018

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Detecting sequence homology at the gene cluster level with MultiGeneBlast

23 May 2018

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Accurate prediction of secondary metabolite gene clusters in filamentous fungi

23 May 2018

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StreptomeDB: a resource for natural compounds isolated from Streptomyces species

23 May 2018

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DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters

23 May 2018

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The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

23 May 2018

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

23 May 2018

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ClusterMine360: a database of microbial PKS/NRPS biosynthesis

23 May 2018

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MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

23 May 2018

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The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity

23 May 2018

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Natural product biosynthetic gene diversity in geographically distinct soil microbiomes.

23 May 2018

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Reprogramming a module of the 6-deoxyerythronolide B synthase for iterative chain elongation

23 May 2018

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Natural products as sources of new drugs over the 30 years from 1981 to 2010

23 May 2018

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FAME, the Flux Analysis and Modeling Environment

23 May 2018

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Computational tools for the synthetic design of biochemical pathways

23 May 2018

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Construction and completion of flux balance models from pathway databases

23 May 2018

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KNApSAcK Family Databases: Integrated Metabolite-Plant Species Databases for Multifaceted Plant Research

23 May 2018

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The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks

23 May 2018

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Tackling antibiotic resistance

23 May 2018

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Recombinatorial biosynthesis of polyketides.

23 May 2018

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Accelerated Profile HMM Searches

23 May 2018

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ChEMBL: a large-scale bioactivity database for drug discovery

23 May 2018

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Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases

23 May 2018

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PKSIIIexplorer: TSVM approach for predicting Type III polyketide synthase proteins

23 May 2018

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

23 May 2018

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MEMOSys: Bioinformatics platform for genome-scale metabolic models

23 May 2018

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Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase

23 May 2018

1 reference

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High-throughput generation, optimization and analysis of genome-scale metabolic models

23 May 2018

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SMURF: Genomic mapping of fungal secondary metabolite clusters

23 May 2018

1 reference

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BAGEL2: mining for bacteriocins in genomic data

23 May 2018

1 reference

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SBSPKS: structure based sequence analysis of polyketide synthases

23 May 2018

1 reference

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BACTIBASE second release: a database and tool platform for bacteriocin characterization

23 May 2018

1 reference

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A protocol for generating a high-quality genome-scale metabolic reconstruction

23 May 2018

1 reference

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Antibiotics for emerging pathogens

23 May 2018

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Automated genome mining for natural products.

23 May 2018

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

23 May 2018

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ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

23 May 2018

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Crystal structure of the termination module of a nonribosomal peptide synthetase

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Metabolic flux analysis and metabolic engineering of microorganisms

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

BACTIBASE: a new web-accessible database for bacteriocin characterization

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

ChEBI: a database and ontology for chemical entities of biological interest

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

NORINE: a database of nonribosomal peptides

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Combinatorial biosynthesis of novel antibiotics related to daptomycin

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

BAGEL: a web-based bacteriocin genome mining tool.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

SEARCHPKS: A program for detection and analysis of polyketide synthase domains.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Big effects from small changes: possible ways to explore nature's chemical diversity.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

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

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system.

23 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Natural product proteomining, a quantitative proteomics platform, allows rapid discovery of biosynthetic gene clusters for different classes of natural products.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2).

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Metabolic impact assessment for heterologous protein production in Streptomyces lividans based on genome-scale metabolic network modeling

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

NRPSsp: non-ribosomal peptide synthase substrate predictor

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Module extension of a non-ribosomal peptide synthetase of the glycopeptide antibiotic balhimycin produced by Amycolatopsis balhimycina

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Active-site residue, domain and module swaps in modular polyketide synthases

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5640684

Editorial: ChemSpider--a tool for Natural Products research

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29062930

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.SYNBIO.2015.12.002

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29062930%20AND%20SRC:MED&resulttype=core&format=json

8 April 2020

1 reference