Useful Resources
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useful scientific resources
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
journals of interest
- ACS Central Science
- ACS Chemical Biology
- Angewandte Chemie International Edition
- Antimicrobial Agents and Chemotherapy
- Biochemistry
- Biochimie
- Cell
- Cell Chemical Biology
- Cell Host & Microbe
- ChemBioChem
- Chemical Science
- Current Opinion in Chemical Biology
- Current Opinion in Microbiology
- Journal of Bacteriology
- Journal of Biological Chemistry
- Journal of Medicinal Chemistry
- Journal of Molecular Biology
- Journal of Natural Products
- Journal of the American Chemical Society
- mBio
- Molecular Cell
- Molecular Microbiology
- Natural Product Reports
- Nature
- Nature Biotechnology
- Nature Catalysis
- Nature Chemical Biology
- Nature Chemistry
- Nature Medicine
- Nature Microbiology
- Nature Methods
- Nature Reviews Drug Discovery
- Nature Reviews Microbiology
- Nature Structural & Molecular Biology
- Organic Letters
- PLOS Biology
- PLOS Pathogens
- Proc. Natl. Acad. Sci. USA
- Science
- Structure
- Trends in Biochemical Sciences
- Trends in Microbiology
resources at Vanderbilt
- Cell Media Facility
- College of LAS Seminars
Department of Biochemistry - Department of Chemistry
- Department of Microbiology
- DNA Sequencing Core (ERML)
- FOM (instrument reservations)
- High-Performance Biological Computing (HPCbio)
- Illinois Directory
- IGB Instrumentation
- Life Sciences Storeroom
- NMR Facilities
- SCS Storeroom (RAL)
- UIUC Webmail
- VANTAGE
safety resources
- 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