Proteins are fundamental to the health and functioning of all living organisms. Protein modifications, which involve the addition or removal of chemical functional groups to proteins, alter protein conformations and often change protein functions. This research introduces a computational framework to evaluate how much more or less likely certain parts of human proteins are to be modified compared to others. These insights can be invaluable for elucidating the molecular mechanisms underlying diseases, such as cancer and Alzheimer's. As a result, the primary impact is anticipated in healthcare and biotechnology. The developed methodology can be extended to proteins from various species, facilitating analyses of protein modification-conformation associations across diverse fields. This broad applicability supports hypothesis generation and evaluation in areas such as agriculture, chemical industries, and environmental sciences. By providing open access to data and tools via a GitHub repository (https://github.com/wodmuer/protmodcon), this study empowers researchers to interrogate protein modification-conformation associations relevant to their specific proteins, modifications, or conformational elements of interest. In summary, this comprehensive analysis of protein modifications from a conformational perspective establishes a foundational resource that can catalyse advancements in health and biotechnology. Furthermore, its applicability to a broad range of organisms holds the potential to drive innovation across diverse sectors, ultimately enhancing the functioning of all living organisms.