Quantifying discrepancies between computationally derived and native (reference) structures is an essential step in the development and comparison of protein modeling and protein-protein docking methods. Measuring conformational differences of proteins or protein complexes is also important in other areas of structural biology such as molecular dynamics and crystallography. There are multiple scores to do that. However, nearly all of them, whether superposition-based (e.g., RMSD) or superposition-free, use distances to measure similarity. CAD-score is conceptually different as it uses physical contacts represented as contact areas. Such representation makes it possible to quantify differences of both structures and surfaces (e.g., protein-protein interfaces and binding sites) using the same framework. A number of studies have found CAD-score to be among the most robust scores. The method is implemented both as a web server and as standalone software available at http://bioinformatics.lt/software/cad-score . Here, we describe how to use the standalone CAD-score software for comparison and analysis of protein structures, interfaces, and binding sites.
Keywords: Contact area; Global similarity score; Interatomic contacts; Local similarity score; Protein structure; Protein-protein interactions; Voronoi tessellation.