Useful Resources

Useful Scientific 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

Fire Extinguisher Training: guide to fire extinguisher types and fire types
NIOSH Pocket Guide to Chemical Hazards: key hazard information on specific chemicals, including properties and toxicity information
Prudent Practices in the Laboratory: publication (free online as e-book) from the National Research Council including extensive safety practices on use of reagents and equipment as well as chemical disposal
Safety in Academic Chemistry Laboratories: brief electronic publication (pdf e-book) by ACS with general practices for specific laboratory techniques; Vanderbilt Biological Safety; Vanderbilt Chemical Safety and Waste disposal