In the realm of protein structural analysis, a formidable challenge looms — the elucidation of missing elements within these intricate biomolecular structures. As researchers venture into the intricate world of protein structures, they frequently encounter voids and gaps, resembling incomplete puzzles awaiting resolution. To tackle this issue, our research initiative harnesses two powerful techniques. The first, known as PepMcConst, operates within a Monte Carlo framework, systematically restoring missing elements within 3D protein structures. This method, acting as a restorative force, effectively reconstructs elusive components, including often-absent C-terminal segments. However, our research is not conducted in isolation, as we also incorporate rapidly-developing methodologies, notably AlphaFold, an AI-driven approach that enhances the precision and speed of protein structure predictions. Our overarching mission is resolute — to safeguard every fragment within the intricate tapestry of protein structures. Through the seamless integration of advanced methodologies, we embark on a transformative journey, poised to unveil the concealed enigmatic dimensions inherent within these molecular enigmas, thereby reshaping the landscape of contemporary science and technology.