When I was working in research, whenever I needed an online molecular biology tool, Pedro’s Molecular Biology Search and Analysis Tools would always be the first place I would go to. Pedro Maldonado Coutinho generated the list when he was a graduate student at Iowa State University of Science and Technology, he has however moved on and is now a professor of Glycogenomics in Marseille, France. Good for him but unfortunately Pedro´s List has not been maintained since. Several alternative sites are available that maintain good lists of links to molecular biology tools that you may want to check out, see below. For literature searches look at my blog on searching the medical literature.
Molecular Biology tools – sites with links
At Expasy, a site created by the Swiss Institute for Bioinformatics, you can find a very extensive collection of links to tools for gene and protein analysis, metabolic pathways, microRNAS etc, and searchable databases (with information on regulatory sites, polyA sites, lipids, biochemical interactions, etc etc).
Another excellent source of links to many tools and databases is the site of the European Bioinformatics Institute in the UK. They claim to maintain the world’s most comprehensive range of freely available and up-to-date molecular data resources.
Another site with links to tools for analysis of DNA, RNA, protein, carbohydrates, metabolomics, genomics, transcription, etc: Internet sources for molecular biologists maintained by Andrew Kropinski (University of Guelph, Ontario, Canada).
Links to tools for sequence analysis, primer design, restriction analysis, as well as various bioinformatics resources: The Bio-Web, this is a non-commercial, educational site.
Links to tools for protein and DNA analysis, biomolecular modeling, bioinformatics & computational tools, phylogeny resources, biochemistry, and biotechnology: CMS Molecular Biology Resource, maintained by Christopher M. Smith (University of California, San Diego) this is a good site but has only been updated till 2002.
Molecular Biology tools – sites with actual tools
A site with a few molecular cloning tools: Molbiotools, maintained by Vladimir Cermak (Charles University, Prague, Czech Republic).
Many companies selling molecular biology products also have useful tools, such as for primer design and restriction analysis. Most are geared toward their own products of course. A pleasant exception is the NEB cutter site that also uses restriction enzymes from other companies.
If you cannot find a tool for a specific task, or are not sure which one to use, it is always worth asking other scientists on ResearchGate.
Let me know in case a site with good links is out there that is not on this list.