Useful Resources

AlphaFold
biomolecular structure predictions

antiSMASH
antibiotics & secondary metabolite analysis shell

Batch Entrez
retrieves large numbers of NCBI records

BLAST
finds regions of similarity between biological sequences

CASTpFold
tool for determining protein topology

EFI – Enzyme Similarity Tool
tool for generation of sequence similarity networks

HMMER
EMBL-EBI search tools using profile hidden Markov Models

HHPred
secondary structure homology prediction

Integrated Microbial Genomics (IMG)
analysis, annotation, and distrubtion of microbial genome datasets

InterPro
functional analysis of proteins by classification into familes, predicting domains and important sites

MicroScope
a web-based platform for comparative microbial genome analysis and manual annotation

MUSCLE
multiple sequence alignment creation

RadicalSAM.org
RadicalSAM.org enables the use of the EFI’s genomic enzymology web tools for studies of the radical SAM superfamily

RODEO
algorithm for the analysis of biosynthetic gene clusters, with an emphasis on RiPPs

SignalP
signal peptide prediction

Skylign
logo creation

STRING
database of known and predicted protein interactions

ARS Culture (NRRL) Collection
searchable online catalog of the NRRL collection of microorganisms

ATCC
nonprofit, global biological resource center and supplier of authenticated cells lines and microorganisms

DSMZ
Leibniz Institute strain collection

Molecular Biology

Codon Usage Database
list of codon usage for different organisms

Expasy-ProtParam
computation of various physical and chemical parameters for a given protein

Expasy-Translate
translation of a nucleotide sequence to a protein sequence

IDT OligoAnalyzer
calculates properties of oligonucleotides

JCat
Java-based codon adaptation tool

NEB Cloning and Synthetic Biology Tools
NEB tools for molecular cloning, DNA assembly and synthetic biology

NEB Tools and Resources
interactive tools from NEB for research and experimental design

Protein Data Bank
repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids

Sequence Manipulation Suite
compiled list of JavaScript programs for generating, formatting and analyzing DNA and protein sequences

BRENDA
Comprehensive Enzyme Information System

Dictionary of Natural Products
structure and biological origin of natural products

Foldseek Search Server
Foldseek Server offers fast and sensitive protein structure alignments against large protein structure collections

MEROPS
information resource for peptidases and the proteins that inhibit them

MIBiG
database of biosynthetic gene clusters

Protein Data Bank
repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids

Sequence Manipulation Suite
compiled list of JavaScript programs for generating, formatting and analyzing DNA and protein sequences

Spectroscopy

ChemCalc Molecular Formula Finder
generate a list of molecular formulas from an accurate mass

Dinesh NMR
peptide NMR tools, including Random coil Proton Chemical shifts

Interactive Peptide Spectral Annotator
analysis of MS/MS data

ProteinProspector
proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments

RESID Database
database of known protein modifications

Unimod
protein modifications for mass spectrometry