The protocol below automatically generates a template coordinate set. It initially places the atoms of the macromolecule along the -axis, with and set to random numbers. The coordinates are then regularized using simulated annealing. The protocol is completely general, and it has been tested for both proteins and nucleic acids.
Disulfide bonds and other covalent links between sequentially distant residues may have to be removed for successful completion of the template generation. Generally, when too many covalent links are present, the structure may get entangled in a knot which will result in poor local geometry. Some experimentation may be required to find out if certain covalent links have to be removed; the goal is to obtain an energy below 1000 kcal mole for the final step of minimization. This protocol has been successfully used with up to three disulfide bridges. However, in the case of bovine pancreatic trypsin inhibitor, removal of the disulfides was required.
Xplor-NIH 2023-11-10