Electronic Resources
Scripting
- Linux in a Nutshell: Great resource for learning how to master the command line
- Sed: Very simple command line text manipulation; best for quick substitutions
- Awk: Simple, column-oriented text processing; best for use on one file
- Perl: Extremely powerful text file manipulation; arguably the best in its class
- Python: User-friendly, object oriented data manipulation
Protocols & General Info
- Open Wet Ware: Sharing of information, know-how, and wisdom among researchers and groups who are working in biology and biological engineering
- HPLC and LC-MS Resources
- Acidity and Basicity Data: Reference data, pKa tables, methods, links
- E. coli genotypes
- Protocol Online
- BRENDA: The Comprehensive Enzyme Information System
Primer Design
- PrimerX: Automated design of mutagenic primers for site-directed mutagenesis
- Stratagene: QuikChange® Primer Design Program
Gene Synthesis
- DNA Works 2.4: Automatic oligonucleotide design for PCR-based gene synthesis
Downloadable Programs
- Foldit: The Baker Lab's interactive protein folding game
- Rosetta@home: The Baker Lab's distributed computing program
- BKChem: Free chemical drawing program
- geneious: DNA and protein sequence analysis tools
- SciFinder Scholar: Search the extensive Chemical Abstracts Databases
- BioKin: Custom software and consulting services for the analysis of chemical, biochemical, and biological data
- Molecular Biology Freeware for Windows
Molecular Visualization Software
Online Servers
- Robetta: Full-chain protein structure prediction server
- BioInfoBank: Gateway to well-benchmarked protein structure and function prediction methods
- SMILES: Translator and structure file generator
- molmovdb.org: Database of Macromolecular Movements
- Zbio.net: PCR Optimization
Databases
- RCSB PDB
- PDBsum: At-a-glance overview of every macromolecular structure deposited in the PDB
- Dynameomics: MD Simulation Database curated by the Daggett Lab
- Spectral Database for Organic Compounds
- eMolecules: Database of molecules
- NIST Chemistry WebBook
- addgene: Non-profit plasmid repository
- Catalytic Site Atlas
- Metal coordination groups in proteins