Applications of Leveling Methods to Properties of Small Molecules and Protein Systems

Despite the advent of high performance computing resources, calculations applied to large systems may remain intractable. Methods to reduce the level of details are therefore essential to allow fast calculations, but also to provide new insights into the systems under study. In this paper, various techniques and application domains related to the leveling of molecular properties through low-resolution, smoothing, denoising, or coarse-graining approaches, are presented. A focus is done on Gaussian smoothing, wavelet multi-resolution analysis, crystallography-based methods, as well as discretization methods. An emphasis is given on the use of smoothed charge density distribution functions and their extrema to generate reduced point charge models (RPCM) of proteins. Molecular dynamics simulations based on RPCMs are reported for three Ubiquitin complexes. Results are discussed based on the ability of such models to generate stable protein-ligand conformations.