FEDER/2: program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space Original Research Article

The computer program, FEDER/2, has been developed to carry out static and dynamic conformational energy analysis of macromolecules by treating dihedral angles as independent variables. The original program, FEDER (H. Wako and N. Gō, J. Comput. Chem. 8 (1987) 625), developed to rapidly calculate first and second derivatives of a conformational energy function with respect to dihedral angles for a single one protein molecule, has been extended by generalizing the tree representation and by revising the program. The tree topology of a molecular system, which is essential to this program, is defined in terms of rigid ‘unit’ and rotatable ‘bond’. Then, algorithms and formulae based on the tree topology are developed to calculate the first and second derivatives. In this revised version of the program we have constructed a library of units, from which a set of data required for a given specific system of molecules is generated. By separating such parts of the program that take care of specifics of various molecular systems into a form of data in the library of units, the main part of the program to calculate the first and second derivatives has become general enough to be applicable to wider types of molecules.