I'm very new here. In fact, it is my first post. I'm a computer scientist which is studying protein structure prediction in ab initio modeling.
My doubt is concern about conversion of protein from dihedral angles representation to Cartesian representation. Where distances, angles and dihedrals of protein are stored? What algorithm is used for it?
I've read about Rosetta ab initio algorithm uses dihedral angles representation and computes energies of protein conformation. Therefore, I understood that it is necessary to convert from dihedral angles representation to Cartesian representation. For this is necessary to give for algorithm information about each atom of protein: distances between atoms connected, value of angle with third atom and dihedral angle with four atom.
In this way, I've implemented SN-Nerf algorithm based on article below:
Jerod Parsons, J. Bradley Holmes, J. Maurice Rojas, Jerry Tsai, Charlie E. M. Strauss (2005). "Practical conversion from torsion space to Cartesian space for in silico protein synthesis". Journal of Computational Chemistry 26 (10): 1063–1068. doi:10.1002/jcc.20237
My representation of atoms of each amino acid was based on CHARMM 27 force-field.
Therefore, my main question is concerned about the parameters and the algorithm are used by Rosetta to convert from dihedral angles representation to Cartesian representation.
I thanks any help.