A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters

Biochemical and Structural Analysis of a Dehydrogenase, KanD2, and an Aminotransferase, KanS2, That Are Responsible for the Construction of the Kanosamine Moiety in Kanamycin Biosynthesis

(2020) Fumitaka Kudo et al.   BIOCHEMISTRY

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

(2020) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences

(2020) Michael A. Skinnider et al.   Nature Communications

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

(2019) Geoffrey D Hannigan et al.   NUCLEIC ACIDS RESEARCH

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

NeuRiPP: Neural network identification of RiPP precursor peptides

(2019) Emmanuel L. C. de los Santos   Scientific Reports

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Dereplication of microbial metabolites through database search of mass spectra

(2018) Hosein Mohimani et al.   Nature Communications

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

(2018) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Actinomycetes: still a source of novel antibiotics

(2017) Olga Genilloud   NATURAL PRODUCT REPORTS

Predictive compound accumulation rules yield a broad-spectrum antibiotic

(2017) Michelle F. Richter et al.   NATURE

A new genome-mining tool redefines the lasso peptide biosynthetic landscape

(2017) Jonathan I Tietz et al.   Nature Chemical Biology

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery

(2017) Mohammad Alanjary et al.   NUCLEIC ACIDS RESEARCH

RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links

(2017) Priyesh Agrawal et al.   NUCLEIC ACIDS RESEARCH

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

(2017) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research

(2017) Chen Zhang et al.   Scientific Reports

Genomics-Inspired Discovery of Three Antibacterial Active Metabolites, Aurantinins B, C, and D from Compost-Associated Bacillus subtilis fmb60

(2016) Jie Yang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Characterization of the aurantimycin biosynthetic gene cluster and enhancing its production by manipulating two pathway-specific activators in Streptomyces aurantiacus JA 4570

(2016) Houyuan Zhao et al.   Microbial Cell Factories

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining

(2015) Xiaoyu Tang et al.   ACS Chemical Biology

Pinensins: The First Antifungal Lantibiotics

(2015) Kathrin I. Mohr et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

(2015) John A. Gerlt et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Going Out on a Limb: Delineating The Effects of β-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues

(2015) Andrew T. Bockus et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products

(2015) Rashed S. Al Toma et al.   NATURAL PRODUCT REPORTS

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Bioengineering Lantibiotics for Therapeutic Success

(2015) Des Field et al.   Frontiers in Microbiology

Identification and characterization of the biosynthetic gene cluster of polyoxypeptin A, a potent apoptosis inducer

(2014) Yanhua Du et al.   BMC MICROBIOLOGY

Alanine Scan of the Peptide Antibiotic Feglymycin: Assessment of Amino Acid Side Chains Contributing to Antimicrobial Activity

(2013) Anne Hänchen et al.   CHEMBIOCHEM

PKMiner: a database for exploring type II polyketide synthases

(2012) Jinki Kim et al.   BMC MICROBIOLOGY

Catalytic Site-Selective Thiocarbonylations and Deoxygenations of Vancomycin Reveal Hydroxyl-Dependent Conformational Effects

(2012) Brandon S. Fowler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Feglymycin is an Inhibitor of the Enzymes MurA and MurC of the Peptidoglycan Biosynthesis Pathway

(2011) Saskia Rausch et al.   CHEMBIOCHEM

Historical Variation of Structural Novelty in a Natural Product Library

(2011) De-Xin Kong et al.   CHEMISTRY & BIODIVERSITY

Synthesis-enabled functional group deletions reveal key underpinnings of amphotericin B ion channel and antifungal activities

(2011) D. S. Palacios et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Modern Natural Products Drug Discovery and Its Relevance to Biodiversity Conservation

(2010) David G. I. Kingston   JOURNAL OF NATURAL PRODUCTS

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

N-Methylation of Peptides: A New Perspective in Medicinal Chemistry

(2008) Jayanta Chatterjee et al.   ACCOUNTS OF CHEMICAL RESEARCH

N-Methyl Scanning Mutagenesis Generates Protease-Resistant G Protein Ligands with Improved Affinity and Selectivity

(2008) Stephen V. Fiacco et al.   CHEMBIOCHEM