A matrix representation for the geometrical algorithm to search the conformational space (GASCOS) for flexible linear molecules

Abstract

Matrix representation has been developed for two successive rotations (α, β) in order to calculate easily the atomic coordinates (as well as non-bonded distances) from the initial molecular geometry and the dihedral angles applied (α, β). It has been shown that the numerical quantities in the matrices involved, can be calculated from the initial molecular configuration. In addition to these matrices only analytic functions were needed with explicit dependence on the dihedral angles (α, β) to calculate the position vectors of the constituting atoms. Hopefully, the generalized method can be adapted to peptide folding with particular emphasis to the side-chain/side chain interaction.