Figure 3
From: NCACO-score: An effective main-chain dependent scoring function for structure modeling
Schematic illustration of the parameters used in the beta sheet geometry propensity potential. A: Left is the representation of backbone atoms and side chain centroid atom of beta sheet. Right is the representation of Cα atoms. Using the representation of Cα atoms, the geometrical features of beta sheet is the same for both parallel and anti-parallel types. B: Four parameters α 1 α 2 β γ for a triplet pair in a beta sheet (parallel) are used to determine the geometrical tendency of beta sheet. α 1 is the angle between two vector (CAi-1CAi and CAiCAi+1), and α 2 is the angle between two vector (CAj-1CAj and CAjCAj+1). Pi denotes the vector in the plane defined by three atoms (CAi-1 CAi CAi + 1) for residue CAi, and Pj denotes the vector in the plane defined by three atoms (CAj-1 CAj CAj + 1) for residue CAj. β is the angle between Pi and Pj. γ is the angle between two vectors (CAi-1CAi and CAj-1CAj). The three blue dotted lines are represented the three distances that are used to define the tendency of forming beta sheet.