Links to Interesting and Useful Biochemical Websites
BRENDA: The Comprehensive Enzyme Information System: http://www.brenda.uni-koeln.de/
This database contains much of the known enzyme information that has been published. Substrates, inhibitors, enzyme kinetic constants and binding affinities are all gathered at this site with the reference material cited. This database is free of all University of Maryland students and faculty.
European Bioinformatics Institute (EBI): http://www.ebi.ac.uk/
This website also includes the Clustal W multiple sequence alignment tool (http://www.ebi.ac.uk/clustalw/)
ExPASy Proteonomics system of the Swiss Institute of Bioinformatics: http://us.expasy.org
At this site, you can search for protein sequences and analyze those sequences with a variety of programs. Also associated with this website is an excellent molecular modeling viewer that can handle structural analysis of protein crystal structures. This viewer is free and has an associated tutorial.
For viewer: http://us.expasy.org/spdbv/
NCBI literature and database search engine: http://www.ncbi.nlm.nih.gov/
At this site, you can search Pubmed/medline - a valuable database of biochemical literature - as well as search for nucleotide and protein sequences. Choose which database you want to search under the Entrez box, or you can search them all. This is also the home of Genbank.
Pedro's Molecular Biology Research Tools: http://www.public.iastate.edu/~pedro/research_tools.html
A listing of molecular biology websites containing tools for searching, analyzing and annotating DNA sequences. Also contained at this website is a listing of biochemistry and chemistry related journals and newsletters.
Primer3 - web based primer design program: http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
Sigma Genosys Oligonucleotide Design Calculator: http://www.genosys.co.uk/oligos/frameset.html
This is a simple tool for calculating the Tm, molecular weight and potential secondary structure of oligonucleotides that may be used as primers.
SIRI: An MSDS database: http://hazard.com/msds/
This is an excellent site to search for the MSDS sheets on all chemicals used in labs or research.
Webcutter: a program to predict where restriction enzyme will cut a particular sequence of DNA.: http://www.carolina.com/webcutter/carolina.asp