{"id":259,"date":"2024-11-21T23:22:44","date_gmt":"2024-11-21T23:22:44","guid":{"rendered":"https:\/\/lab.prd.vanderbilt.edu\/mitchell-lab\/?page_id=259"},"modified":"2025-10-03T23:55:17","modified_gmt":"2025-10-04T05:55:17","slug":"useful-resources","status":"publish","type":"page","link":"https:\/\/lab.vanderbilt.edu\/mitchell-lab\/useful-resources\/","title":{"rendered":"Useful Resources"},"content":{"rendered":"
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looking for the group meeting schedule? click here<\/a><\/h3>\n<\/div>\n<\/div>\n
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Useful Scientific Resources<\/h2>\n<\/div>\n<\/div>\n
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Bioinformatics<\/h3>\n
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AlphaFold<\/a><\/dt>\n
biomolecular structure predictions<\/dd>\n
antiSMASH<\/a><\/dt>\n
antibiotics & secondary metabolite analysis shell<\/dd>\n
Batch Entrez<\/a><\/dt>\n
retrieves large numbers of NCBI records<\/dd>\n
BLAST<\/a><\/dt>\n
finds regions of similarity between biological sequences<\/dd>\n
CASTpFold<\/a><\/dt>\n
tool for determining protein topology<\/dd>\n
Consurf<\/a><\/dt>\n
identifies conserved residues in homologous proteins<\/dd>\n
EFI – Enzyme Similarity Tool<\/a><\/dt>\n
tool for generation of sequence similarity networks<\/dd>\n
HMMER<\/a><\/dt>\n
EMBL-EBI search tools using profile hidden Markov Models<\/dd>\n
HHPred<\/a><\/dt>\n
secondary structure homology prediction<\/dd>\n
Integrated Microbial Genomics (IMG)<\/a><\/dt>\n
analysis, annotation, and distrubtion of microbial genome datasets<\/dd>\n
InterPro<\/a><\/dt>\n
functional analysis of proteins by classification into familes, predicting domains and important sites<\/dd>\n
MicroScope<\/a><\/dt>\n
a web-based platform for comparative microbial genome analysis and manual annotation<\/dd>\n
MUSCLE<\/a><\/dt>\n
multiple sequence alignment creation<\/dd>\n
RADAR<\/a><\/dt>\n
repeat detection in proteins<\/dd>\n
RadicalSAM.org<\/a><\/dt>\n
RadicalSAM.org enables the use of the EFI’s genomic enzymology web tools for studies of the radical SAM superfamily<\/dd>\n
Regular expression cheat sheet<\/a><\/dt>\n
reference tables for basic regex<\/dd>\n
RODEO<\/a><\/dt>\n
algorithm for the analysis of biosynthetic gene clusters, with an emphasis on RiPPs<\/dd>\n
SignalP<\/a><\/dt>\n
signal peptide prediction<\/dd>\n
Skylign<\/a><\/dt>\n
logo creation<\/dd>\n
STRING<\/a><\/dt>\n
database of known and predicted protein interactions<\/dd>\n<\/dl>\n<\/div>\n
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Microbiology<\/h3>\n
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ARS Culture (NRRL) Collection<\/a><\/dt>\n
searchable online catalog of the NRRL collection of microorganisms<\/dd>\n
ATCC<\/a><\/dt>\n
nonprofit, global biological resource center and supplier of authenticated cells lines and microorganisms<\/dd>\n
DSMZ<\/a><\/dt>\n
Leibniz Institute strain collection<\/dd>\n<\/dl>\n

Molecular biology<\/h3>\n
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Codon Usage Database<\/a><\/dt>\n
list of codon usage for different organisms<\/dd>\n
Expasy-ProtParam<\/a><\/dt>\n
computation of various physical and chemical parameters for a given protein<\/dd>\n
Expasy-Translate<\/a><\/dt>\n
translation of a nucleotide sequence to a protein sequence<\/dd>\n
IDT OligoAnalyzer<\/a><\/dt>\n
calculates properties of oligonucleotides<\/dd>\n
JCat<\/a><\/dt>\n
Java-based codon adaptation tool<\/dd>\n
NEB Cloning and Synthetic Biology Tools<\/a><\/dt>\n
NEB tools for molecular cloning, DNA assembly and synthetic biology<\/dd>\n
NEB Tools and Resources<\/a><\/dt>\n
interactive tools from NEB for research and experimental design<\/dd>\n
Protein Data Bank<\/a><\/dt>\n
repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids<\/dd>\n
Sequence Manipulation Suite<\/a><\/dt>\n
compiled list of JavaScript programs for generating, formatting and analyzing DNA and protein sequences<\/dd>\n<\/dl>\n<\/div>\n
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Reference Databases<\/h3>\n
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BRENDA<\/a><\/dt>\n
Comprehensive Enzyme Information System<\/dd>\n
Dictionary of Natural Products<\/a><\/dt>\n
structure and biological origin of natural products<\/dd>\n
MEROPS<\/a><\/dt>\n
information resource for peptidases and the proteins that inhibit them<\/dd>\n
MIBiG<\/a><\/dt>\n
database of biosynthetic gene clusters<\/dd>\n
PubChem<\/a><\/dt>\n
information on the biological activities of small molecules<\/dd>\n
PubMed<\/a><\/dt>\n
free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics<\/dd>\n
SciFinder<\/a><\/dt>\n
CAS database of chemical and bibliographic information<\/dd>\n<\/dl>\n

Spectroscopy<\/h3>\n
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ChemCalc Molecular Formula Finder<\/a><\/dt>\n
generate a list of molecular formulas from an accurate mass<\/dd>\n
Dinesh NMR<\/a><\/dt>\n
peptide NMR tools, including Random coil Proton Chemical shifts<\/dd>\n
Interactive Peptide Spectral Annotator<\/a><\/dt>\n
analysis of MS\/MS data<\/dd>\n
ProteinProspector<\/a><\/dt>\n
proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments<\/dd>\n
RESID Database<\/a><\/dt>\n
database of known protein modifications<\/dd>\n
Unimod<\/a><\/dt>\n
protein modifications for mass spectrometry<\/dd>\n<\/dl>\n<\/div>\n<\/div>\n
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Journals of Interest<\/h2>\n<\/div>\n<\/div>\n
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ACS Central Science<\/a><\/dd>\n
ACS Chemical Biology<\/a><\/dd>\n
Angewandte Chemie International Edition<\/a><\/dd>\n
Antimicrobial Agents and Chemotherapy<\/a><\/dd>\n
Biochemistry<\/a><\/dd>\n
Cell<\/a><\/dd>\n
Cell Chemical Biology<\/a><\/dd>\n
Cell Host & Microbe<\/a><\/dd>\n
ChemBioChem<\/a><\/dd>\n
Chemical Science<\/a><\/dd>\n
Current Opinion in Chemical Biology<\/a><\/dd>\n
Current Opinion in Microbiology<\/a><\/dd>\n
Journal of Bacteriology<\/a><\/dd>\n<\/dl>\n<\/div>\n
Journal of Biological Chemistry<\/a>
\nJournal of Medicinal Chemistry<\/a>
\nJournal of Molecular Biology<\/a>
\nJournal of Natural Products<\/a>
\nJournal of the American Chemical Society<\/a>
\nmBio<\/a>
\nMolecular Cell<\/a>
\nMolecular Microbiology<\/a>
\nNatural Product Reports<\/a>
\nNature<\/a>
\nNature Biotechnology<\/a>
\nNature Catalysis<\/a>
\nNature Chemical Biology<\/a><\/div>\n
Nature Chemistry<\/a>
\nNature Medicine<\/a>
\nNature Microbiology<\/a>
\nNature Methods<\/a>
\nNature Reviews Drug Discovery<\/a>
\nNature Reviews Microbiology<\/a>
\nNature Structural & Molecular Biology<\/a>
\nOrganic Letters<\/a>
\nPLOS Biology<\/a>
\nPLOS Pathogens<\/a>
\nProc. Natl. Acad. Sci. USA<\/a>
\nScience<\/a>
\nStructure<\/a><\/div>\n<\/div>\n
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Resources at Vanderbilt<\/h2>\n<\/div>\n<\/div>\n
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Department of Biochemistry<\/a><\/dd>\n
Department of Chemistry<\/a><\/dd>\n
NMR Facilities<\/a>
\nVanderbilt Directory<\/a><\/dd>\n
VANTAGE<\/a>
\nVICB Seminars<\/a><\/dd>\n<\/dl>\n<\/div>\n<\/div>\n
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Safety Resources<\/h2>\n<\/div>\n<\/div>\n
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Environmental Health and Safety<\/a> (EHS)<\/dt>\n<\/dl>\n
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Fire Extinguisher Training<\/a><\/dt>\n
guide to fire extinguisher types and fire types<\/dd>\n
NIOSH Pocket Guide to Chemical Hazards<\/a><\/dt>\n
key hazard information on specific chemicals, including properties and toxicity information<\/dd>\n
Prudent Practices in the Laboratory<\/a><\/dt>\n
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<\/dd>\n
Safety in Academic Chemistry Laboratories<\/a><\/dt>\n
brief electronic publication (pdf e-book) by ACS with general practices for specific laboratory techniques<\/dd>\n
Vanderbilt Biological Safety<\/a><\/strong><\/dd>\n
Vanderbilt Chemical Safety and Waste disposal<\/a><\/strong><\/dd>\n
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