The objective of this website is to predict the stability of the collagen triple-helix from amino acid sequence using an algorithm based on experimental host-guest peptide thermal stability data.
The algorithm can be applied to a peptide with a repeating (Gly-X-Y)n sequence, to predict the melting temperature, Tm, under standard conditions (c=1mg/ml; PBS, pH 7; average heating rate 0.1°/min). If the terminal groups of the peptide are blocked, this must be indicated, since it increases the stability.
Although collagen molecules are long and consist of multiple domains, the algorithm can be applied to predict the variations in triple-helix stability along a collagen molecule. In this case, the relative stability representing a 5-tripeptide average can be visualized as a graph. The precise average values are also given in a table, and can be used for further analysis. In this case, the values reflect relative thermal stability, but cannot be directly related to collagen melting temperatures! While every effort has been made to ensure the accuracy of the information reported on this site, we make no guarantees and strongly suggest that you double check all sequences and information obtained here before using them.
Data entry format:
Enter a sequence in any format using a one-letter amino acid standard code. You can use "O" for hydroxyproline. Anything like "GPOGARGMOGPAGPOGAR" or "GPO-GAR-GRE-GTA-GTT-GAA-GPO" or "2536GPO----GAr-GRE-#25-gta-GTT-GAA-GPO-xxx" will work. Any simbols different from one-letter amino acid code, including numbers and special symbols will be ignored. If your sequence has a braekage in G-X-Y repeating pattern, all seuence after the breakage will be ignored. The best thing to do is to check the resulting length or your sequence. The sequences may be entered with O as hydroxyproline (Hyp). Alternatively, since Pro are typically post-translationally modified to Hyp in the Y position, a sequence with only Pro residues can be entered, and the program will modify all Pro in the Y positions to Hyp if the appropriate box is checked. When entering homotrimeric sequences please make sure you checked an appropriate ceckbox. For heterotrimers you must enter sequences of equal length and uncheck the checkbox, otherwise only Chain A will be used for the calculations.
The algorithm is described in Persikov, A., Ramshaw, J.A. and Brodsky, B., J. Biol. Chem. (2005) Prediction of collagen stability from amino acid sequence. If you are publishing results that include collagen stability predictions or collagen-like peptides designed using this website, please reference the Collagen Stability Calculator using this citation.