When I was working in research, whenever I needed any 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 therefore 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 (in order of relevance)
Currently the best site available with links to tools for analysis of DNA, RNA, and 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
Although many of the links on Pedro´s list are broken, they may give you ideas of what type of tools are out there so you can google for newer versions or the correct links.
Molecular Biology tools – sites with actual tools
Tools for gene and protein analysis, CRISPR and siRNA design, metabolic pathways, primer design, restriction analysis: Genome Compiler, this is a commercial site but has many useful 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.
Let me know in case a site with good links is out there that is not on this list.