bioinformatics

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

Consurf

identifies conserved residues in homologous proteins

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

RADAR

repeat detection in proteins

RadicalSAM.org

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

Regular expression cheat sheet

reference tables for basic regex

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

microbiology

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

reference databases

BRENDA

Comprehensive Enzyme Information System

Dictionary of Natural Products

structure and biological origin of natural products

MEROPS

information resource for peptidases and the proteins that inhibit them

MIBiG

database of biosynthetic gene clusters

PubChem

information on the biological activities of small molecules

PubMed

free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics

SciFinder

CAS database of chemical and bibliographic information

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