The triple helix is a unique and important protein fold present in the collagen family of proteins, a large family of extracellular matrix proteins abundant in the human body. Collagen mimetic peptides (CMPs) are currently of great utility for studying the structure and biological functions of the collagen triple helix. Chapter 1 is a review of recent advances in the field of collagen mimetic peptide design with an overview of CMPs in structural, biological, and biomaterial applications. Chapter 2 will discuss pairwise amino acid interactions studied in a methodical manner for deconvoluting the stability each interaction contributes to the triple helix. This study both increased our understanding of the collagen triple helix structure as well as contributed to the training set for an algorithm which predicts the stability and specificity of triple helices with great accuracy for natural amino acids. This algorithm allows one to utilize pairwise interactions to design heterotrimers with predictable stability and specificity of assembly. Chapter 3 presents covalent capture methodology as a means for stabilizing CMP triple helices. This method uses the pairwise interactions K-D and K-E studied in Chapter 1 to first direct helix assembly, followed by amide bond formation to cross-link the helix. Covalent capture removes the problematic monomer to trimer equilibrium that causes slow folding rates, mixtures of triple helix compositions, and limits in vivo applications of CMPs. Applications of CMPs is next explored, by studying protein interactions with collagen and designing collagen targeting peptides. Chapter 4 utilizes covalent capture to limit the degradation of a CMP by matrix metalloproteinas-1 (MMP-1). Covalent capture limits the rotational movement of the individual CMP peptide strands; therefore, comparison of this covalently captured to a supramolecular peptide gives valuable insight into the collagenolytic mechanism of MMPs. Additionally, development of a peptide with limited degradation by MMPs would be of utility for peptide biomaterial applications. Finally, Chapter 5 will discuss our recent advances towards a collagen targeting peptide (CTP) with specificity for a single collagen type. CTPs have been shown in the literature to be useful for targeting collagen for imaging and drug delivery but with no specificity for collagen type. We design CTPs to target collagen types 1-3 using rational design of pairwise interactions and a scoring function (from Chapter 2) and evaluate these CTP designs via folding with CMPs, binding to extracted natural collagens, and histological staining. CMP helices are of great utility for the continued study of the natural collagen structure and its many protein interactions and diseases. Advances in all these areas have resulted in significant improvements to our understanding and control of this important class of protein.