Fig. 1: The pipeline for measuring and locating secondary structure variations by calculating Geometric Characteristics among residues within compared protein pair.
From: Measuring and locating the changes in protein structure using MELO
a preprocessing the structure preparation and representation. S-W- & US-align-based algorithms were used to align two protein sequences (SA and SB), establishing the residue-level correspondences and ensuring a precise mapping promoting downstream analyses. b computing geometric characteristics of studied amino acids. Key geometric characteristics of amino acids were calculated for both SA and SB, including: bend angles (KAPPA), dihedral angles (ALPHA), peptide backbone torsion angles (PHI and PSI), water exposed surface (ACC), etc. All characteristics were encoded into vectors (such as V1, V1’ for SA and V2, V2’ for SB). c depicting PLOTVSS based on geometric characteristics among residues. Variations in secondary structure were located using PLOTVSS. The darker the residue’s color was, the higher its ci value was, which reflected greater variation in its corresponding secondary structure. Moreover, the PLOTVSS showed the type of secondary structure in SA and SB, with the classification information described in Supplementary Fig. S25. d calculating VSSmeasur based on the geometric characteristics among residues. VSSmeasur scores were calculated to quantify overall secondary structure variation. Particularly, the closer the VSSmeasur is to 1, the more different the secondary structures of two studied proteins are.
