We will discuss the analysis of membrane remodeling by proteins and peptides using multi-scale computational methods; these include mainly molecular dynamics simulations at atomistic and coarse-grained levels, although we will also touch upon analyses using lattice models and a mean- field theory. The discussions will cover several systems that we have analyzed in recent studies, which include the SAR1 protein from the COPII machinery and the ESCRTIII complex; we will also briefly discuss how protein condensates interact with lipid membranes, especially in terms of their mutual influence on morphology and phase behaviors. These examples illustrate different molecular properties and mechanisms that are potentially relevant to membrane remodeling, as well as the values and limitations of various computational methodologies in such context.