RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

(2020) Mark C. Walker et al.   BMC GENOMICS

Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides

(2019) Graham A. Hudson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic 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

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

(2019) Rémi Zallot et al.   BIOCHEMISTRY

Nonribosomal Peptide Extension by a Peptide Amino-Acyl tRNA Ligase

(2019) Zhengan Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RiPP antibiotics: biosynthesis and engineering potential

(2018) Graham A Hudson et al.   CURRENT OPINION IN MICROBIOLOGY

Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics

(2018) Christopher J. Schwalen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural noncanonical protein splicing yields products with diverse β-amino acid residues

(2018) Brandon I. Morinaka et al.   SCIENCE

Enzymatic Reconstitution and Biosynthetic Investigation of the Lasso Peptide Fusilassin

(2018) Adam J. DiCaprio et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Charting an Unexplored Streptococcal Biosynthetic Landscape Reveals a Unique Peptide Cyclization Motif

(2018) Leah B. Bushin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily

(2017) Christopher J. Schwalen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides

(2017) Tyler L. Grove et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

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

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

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

(2017) Katherine M. Davis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthetic Timing and Substrate Specificity for the Thiopeptide Thiomuracin

(2016) Zhengan Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A

(2016) Swapnil V. Ghodge et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Lasso Peptide Biosynthetic Protein LarB1 Binds Both Leader and Core Peptide Regions of the Precursor Protein LarA

(2016) Wai Ling Cheung et al.   ACS Central Science

Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

(2015) Qi Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles

(2015) Courtney L. Cox et al.   BMC GENOMICS

PqqD Is a Novel Peptide Chaperone That Forms a Ternary Complex with the RadicalS-Adenosylmethionine Protein PqqE in the Pyrroloquinoline Quinone Biosynthetic Pathway

(2015) John A. Latham et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products

(2015) Kyle L. Dunbar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Structure and biosynthesis of a macrocyclic peptide containing an unprecedented lysine-to-tryptophan crosslink

(2015) Kelsey R. Schramma et al.   Nature Chemistry

HMMER web server: 2015 update

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

The Pfam protein families database: towards a more sustainable future

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

Structure and mechanism of lanthipeptide biosynthetic enzymes

(2014) Wilfred A van der Donk et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB

(2014) Manuel A. Ortega et al.   NATURE

Database resources of the National Center for Biotechnology Information

(2014)   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Recognition Sequences and Substrate Evolution in Cyanobactin Biosynthesis

(2014) Debosmita Sardar et al.   ACS Synthetic Biology

Intrigues and Intricacies of the Biosynthetic Pathways for the Enzymatic Quinocofactors: PQQ, TTQ, CTQ, TPQ, and LTQ

(2013) Judith P. Klinman et al.   CHEMICAL REVIEWS

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

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

Identification of distinct nisin leader peptide regions that determine interactions with the modification enzymes NisB and NisC

(2013) Rustem Khusainov et al.   FEBS Open Bio

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

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

Evolution of lanthipeptide synthetases

(2012) Q. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners

(2011) Daniel H Haft   BMC GENOMICS

Biological Systems Discovery In Silico: Radical S-Adenosylmethionine Protein Families and Their Target Peptides for Posttranslational Modification

(2011) D. H. Haft et al.   JOURNAL OF BACTERIOLOGY

Substrate Recognition and Specificity of the NisB Protein, the Lantibiotic Dehydratase Involved in Nisin Biosynthesis

(2011) Antonino Mavaro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery and Assembly-Line Biosynthesis of the Lymphostin Pyrroloquinoline Alkaloid Family of mTOR Inhibitors in Salinispora Bacteria

(2011) Akimasa Miyanaga et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family

(2010) Daniel H Haft et al.   BMC BIOLOGY

How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic

(2009) Catherine A Regni et al.   EMBO JOURNAL

Structural and Functional Dissection of the Heterocyclic Peptide Cytotoxin Streptolysin S

(2009) Douglas A. Mitchell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH