Collagen triple helix motif is found widely in structural proteins of the extracellular matrix and in an increasing set of non-collagenous proteins, many of which are involved in host-defense function. In contrast to globular proteins, the relation among sequence, structure, and stability is simpler and better defined for the linear collagen triple helix. The close packing of three supercoiled chains in the collagen triple helix generates a requirement for Gly as every third amino acid residue in collagen sequence.
The collagen triple helix is not uniform in structure or stability. Experimental thermal stability data obtained from host-guest peptides is integrated here to produce an algorithm for predicting global melting temperatures of collagen triple helical peptides and short fragments and for detecting modulations in relative stability along a collagen chain.
The collagen stability algorithm is available here to all users for calculation of global stability of peptides and local stability variations in collagens and collagen-like domains. Please choose one of the two options.
Predict melting temperature (Tm) of short peptides
If you are working on designing short collagen peptides (<90 amino acid residues in each chain), you may want to use "Predict Tm" option. A good agreement was observed between predicted and observed stabilities of a number of collagen peptides (see References). It is always a good idea to run your sequence trough our predictor before spending your time and money on making peptides.
Generate relative stability profile for longer collagen sequences
If you are interested in local stability variations along full-length collagens and its relation to collagen functional domains or mutation sites, you should use the "Stability Profile Generator". The variations in stability along the collagen chain appear related to known functional sites, and high stability is achieved through a combination of stabilizing molecular mechanisms. It is also allowed now to predict stability of collagen heterotrimers, which model better Type I, IV, V and other collagens. There is no size limit in this module. Please check your sequences and also read our help before submitting.