Carbon nanomaterials are receiving an increasingly large interest in a variety of fields, including also nanomedicine. In this area, much attention is devoted to investigating and modeling the behavior of these nanomaterials when they interact with biological fluids and with biological macromolecules, in particular proteins and oligopeptides. The interaction with these molecules is in fact crucial to understand and predict the efficacy of nanomaterials as drug carriers or therapeutic agents as well as their potential toxicity when they occupy the active site of a protein or severely affect the secondary and tertiary structure, or even the local dynamics, thus inhibiting their biological function. In this review, therefore, we describe the most recent work carried out in the last few years to model the interaction between carbon nanomaterials, either pristine or functionalized, and proteins or oligopeptides using classical atomistic methods, mainly molecular dynamics simulations. The attention is focused on 0-dimensional fullerenes, mainly C60, on 1-dimensional carbon nanotubes, mostly the single-walled armchair and some chiral ones, and on 2-dimensional graphene and graphyne, the latter containing also sp hybridized atoms in addition to the sp2 ones common to the other carbon nanomaterials. •Atomistic computer simulations can provide important information about protein adsorption on nanostructured materials.•Charged residues such as lysine, and in particular arginine, may interact very efficiently with hydrophobic carbon nanomaterials, even more than aromatic residues.•Nanomaterials can interact with proteins by occupying their active sites, by changing their secondary or tertiary structure or by affecting their intramolecular dynamics.