SURPASS is a new coarse-grained model of protein structure. Deep reduction of the number of atoms in the representation results in a powerful computational speed-up and in this context ranks the model as a low resolution.
The number of pseudoresidues present in the modeled system corresponds to polipeptide chain size and is equal to N-3, where N is the number of amino acids in the sequence. The positions of pseudo residues are defined by averaging the coordinates of short secondary structure fragments. These fragments are replaced by a single center of interactions. The choice of four residue averaging is crucial for the local geometry of the model because leads to an almost linear shape of the SURPASS fragments representing helices or beta strands.
The SURPASS representation assumes three types of pseudo atoms depending on secondary structure assignment of the averaged fragments of protein structure:
- pseudo atom H (helix-like) for helical (HHHH) or almost helical (HHHC, CHHH) fragments
- pseudo atom S (like β-strand) representing centers of mass of EEEE, EEEC or CEEE, fragments
- pseudo atom C (coil-like) for all remaining secondary structure combinations (H, E and C)