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

Matrix representation has been developed for two successive rotations (alph a, beta) in order to calculate easily the atomic coordinates (as well as no n-bonded distances) from the initial molecular geometry and the dihedral an gles applied (alpha, beta). It has been shown that the numerical quantities in the matrices involved, can be calculated from the initial molecular con figuration. In addition to these matrices only analytic functions were need ed with explicit dependence on the dihedral angles (alpha, beta) to calcula te the position vectors of the constituting atoms. Hopefully, the generaliz ed method can be adapted to peptide folding with particular emphasis to the side-chain/side chain interaction. (C) 2001 Elsevier Science B.V. All righ ts reserved.