Construction of an In Silico Model to Study the Molecular Functions of Type I Collagen.

Modeling of fibrillar collagen such as type I collagen is challenging mainly due to the large size of this protein, its peculiar secondary structure of polyproline II type, found mainly in extracellular matrix proteins, and the presence of posttranslational modifications essential to its function. In this chapter, we present a protocol that allows us to model, at the atomic level, the three-dimensional structure of type I collagen with the THeBuScr and SIDEpro software. The resulting conformation could be used for further molecular docking or molecular dynamics investigations.