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Biology-related tools


RCSB Protein Data Bank

  • International database of 3D biological macromolecules

ExPASy Proteomics server

  • links to many pages to calculate parameters of your favorite proteins


  • E. coli genome site; get sequences, see the position of your gene in the chromosome, and other fun stuff

Biopolymer calculator

  • calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein

Novagen pET vector table

  • table with links to properties/sequences of pET vectors
  • note: slow to load

Protein Prospector

  • UCSF mass spec site to search fragments, etc. to identify your protein

mFold by Michael Zuker.

  • This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.

More good stuff on the Synthetic Biology:Tools page.

Also see Science Web Resources.





New England Biolabs


MIT Links

MIT website

MIT Biology department website

MIT webmail

  • Login required

MIT ECAT ordering

  • Certificate required
  • can also get to Sciquest from here and order from GE Healthcare (formerly Amersham), PerkinElmer, Qiagen, Roche Applied Science, USA Scientific, Newark InOne, Sigma-Aldrich, Invitrogen (coming soon) using your MIT account number instead of a credit card.
  • For instructions on how to use ECAT, see the FAQs page.


  • Purchase orders, requisitions, etc. Certificate required.

Biopolymers facility

  • DNA sequencing, mass spectrometry, protein sequencing, peptide synthesis.