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

Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products

(2016) Evelyn M. Molloy et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Using Genomics for Natural Product Structure Elucidation

(2016) Jonathan I. Tietz et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II

(2016) Julian D. Hegemann et al.   Molecular BioSystems

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

(2016) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

(2016) Michael A. Skinnider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lasso Peptides: An Intriguing Class of Bacterial Natural Products

(2015) Julian D. Hegemann et al.   ACCOUNTS OF CHEMICAL RESEARCH

Construction of Lasso Peptide Fusion Proteins

(2015) Chuhan Zong et al.   ACS Chemical Biology

Characterization of Sviceucin from Streptomyces Provides Insight into Enzyme Exchangeability and Disulfide Bond Formation in Lasso Peptides

(2015) Yanyan Li et al.   ACS Chemical Biology

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

Structure, Bioactivity, and Resistance Mechanism of Streptomonomicin, an Unusual Lasso Peptide from an Understudied Halophilic Actinomycete

(2015) Mikhail Metelev et al.   CHEMISTRY & BIOLOGY

Structural analysis of leader peptide binding enables leader-free cyanobactin processing

(2015) Jesko Koehnke et al.   Nature Chemical Biology

Minimum Information about a Biosynthetic Gene cluster

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

A prevalent peptide-binding domain guides ribosomal natural product biosynthesis

(2015) Brandon J Burkhart et al.   Nature Chemical Biology

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

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

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase

(2015) Theodoros Goulas et al.   Scientific Reports

The peptidylarginine deiminase gene is a conserved feature of Porphyromonas gingivalis

(2015) Giorgio Gabarrini et al.   Scientific Reports

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Site-Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin

(2014) Rashed S. Al Toma et al.   CHEMBIOCHEM

Lassomycin, a Ribosomally Synthesized Cyclic Peptide, Kills Mycobacterium tuberculosis by Targeting the ATP-Dependent Protease ClpC1P1P2

(2014) Ekaterina Gavrish et al.   CHEMISTRY & BIOLOGY

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

(2014) James R Doroghazi et al.   Nature Chemical Biology

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation

(2014) Marcel Zimmermann et al.   Chemical Science

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Discovery and Characterization of an Isopeptidase That Linearizes Lasso Peptides

(2013) Mikhail O. Maksimov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

NMR as an Effective Tool for the Structure Determination of Lasso Peptides

(2012) Xiulan Xie et al.   CHEMBIOCHEM

Lasso peptides: structure, function, biosynthesis, and engineering

(2012) Mikhail O. Maksimov et al.   NATURAL PRODUCT REPORTS

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Precursor-centric genome-mining approach for lasso peptide discovery

(2012) M. O. Maksimov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of a conserved threonine residue in the leader peptide of lasso peptide precursors

(2011) Si Jia Pan et al.   CHEMICAL COMMUNICATIONS

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Genomics-inspired discovery of natural products

(2010) Jaclyn M Winter et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

(2008) Christine Fong et al.   BMC BIOINFORMATICS

Cloning, Expression, and Biochemical Characterization of Streptomyces rubellomurinus Genes Required for Biosynthesis of Antimalarial Compound FR900098

(2008) Andrew C. Eliot et al.   CHEMISTRY & BIOLOGY