NP.searcher statistics

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NP.searcher specifications

Information


Unique identifier OMICS_09246
Name NP.searcher
Alternative name Natural products search engine
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Output data Simplified Molecular Input Line Entry Specifications (SMILES) of the predicted possible polyketide and nonribosomal peptide natural products
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline David H. Sherman

Information


Unique identifier OMICS_09246
Name NP.searcher
Alternative name Natural products search engine
Interface Web user interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Output data Simplified Molecular Input Line Entry Specifications (SMILES) of the predicted possible polyketide and nonribosomal peptide natural products
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline David H. Sherman

Publication for Natural products search engine

NP.searcher citations

 (15)
library_books

Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential

2017
Front Pharmacol
PMCID: 5702503
PMID: 29209209
DOI: 10.3389/fphar.2017.00828

[…] areas of the extant biosynthetic diversity. A range of systems have been developed to predict the substrate specificities of NRPS adenylation domains (Röttig et al., ; Prieto et al., ). Tools such as NP.searcher and antiSMASH individual monomer predictions are then combined to give a rough idea of the core scaffold of a nonribosomal peptide. Simultaneously, advancement in mass spectrometry gives e […]

library_books

SBSPKSv2: structure based sequence analysis of polyketide synthases and non ribosomal peptide synthetases

2017
Nucleic Acids Res
PMCID: 5570206
PMID: 28460065
DOI: 10.1093/nar/gkx344

[…] al analysis (–). Recent reviews on computational methods for natural product discovery, have compared various features of SBSPKS and other similar bioinformatics tools like AntiSMASH (), ClusScan (), NP.Searcher () and SMURF (), and have provided overviews on utilities of such tools in genome mining studies (,). Since the first version of SBSPKS was released, advances in high throughput technologi […]

library_books

Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism

2017
PMCID: 5625732
PMID: 29062956
DOI: 10.1016/j.synbio.2017.02.002

[…] art of a complete peptide, and can be deduced based on the mass shift pattern, and subsequently screened against predicted substrate specificities of NRPSs, obtained from tools such as antiSMASH and NP.searcher . Later Pep2Path was developed to automatize the detection of BGCs responsible for the amino acid sequence tags based on a Bayesian probabilistic scoring algorithm. MS-guided discovery of […]

library_books

Spotlight on Antimicrobial Metabolites from the Marine Bacteria Pseudoalteromonas: Chemodiversity and Ecological Significance

2016
Mar Drugs
PMCID: 4962019
PMID: 27399731
DOI: 10.3390/md14070129

[…] and hybrid NRPS-PKS pathways exhibit repeated motifs in genomic nuclear sequences, they have led to the development of powerful bioinformatics programs such as antiSMASH [], NapDos [], SBSPKS [], or Np.searcher []. Moreover, the description of a specificity-conferring code in the NRPS A-domain [] has resulted in the development of specialised chemical structure prediction tools, e.g., NRPS predic […]

library_books

Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type I Polyketide Synthases Derived from Marine Microbiomes

2016
Mar Drugs
PMCID: 4849084
PMID: 27092515
DOI: 10.3390/md14040080

[…] eliable predictive models. In the case of PKs, substrate redundancy makes reliable prediction somewhat more challenging []. Nevertheless, refined predictive models were incorporated in antiSMASH, and NP.searcher [] as well as in more specific tools like NRPSpredictor2 (nrps.informatik.uni-tuebingen.de) [], SBSPKS (http://www.nii.ac.in/~pksdb/sbspks/master.html) [] and NRPS-PKS-substrate-predictor […]

library_books

In silico methods for linking genes and secondary metabolites: The way forward

2016
PMCID: 5640692
PMID: 29062931
DOI: 10.1016/j.synbio.2016.03.001

[…] essentially used a knowledge based approach, for deriving prediction rules based on experimentally characterized PKS and NRPS gene clusters. The tools like NRPS-PKS, SBSPKS, ASMPKS/MAPSI, ClustScan, NP.Searcher, NRPSpredictor, PKS/NRPS and PKMiner permit semi-automatic identification and annotation of PKS, NRPS or PKS-NRPS hybrid gene clusters. In addition to annotating the domains of multi-domai […]

Citations

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NP.searcher institution(s)
Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA; Departments of Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA

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