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
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

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

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
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

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