Rigid body minimization

Orientational Sampling and Rigid-Body Minimization in Molecular Docking. 

Figure 11. The combiBUILD algorithm (a) Starting point is a scaffold modeled into its target receptor. CombiBUILD goes over a database of possible reactants to add to the scaffold (b) CombiBUILD performs a systematic rotational search on each reactant (typically in 10-15 increments within the low energy minima for each torsion type), pruning for intramolecular clashes and bumps to make the search more efficient (c) CombiBUILD performs a rigid body minimization on each possible component conformation, scores it with a force-field scheme.

Kuntz. Orientational sampling and rigid-body minimization in molecular docking. PROTEINS Structure, Function and Genetics, 17 266-278, 1993. 

After a complete cycle of mean field optimization of side-chain conformation, a rigid-body minimization is performed on the resultant coordinates of the interacting protein molecules. Only interface residues whose C[1 atoms (Cot for Gly) are within 15 A of the CfS atom of the other molecule are included in the minimization. The larger molecule is kept stationary while the three rotational and three translational degrees of freedom of the smaller molecule are moved according to the path determined by the derivatives to minimize the intermolecular interaction energy. The steepest descents approach for minimization is used. 

G. Marius Clore, Accurate and rapid docking of protein-protein complexes on the basis of inter-molecular nuclear Overhauser enhancement data and dipolar couphngs by rigid body minimization. Proceedings of the National Academy of Sciences USA, 97 (2000), 9021-9025. 

Bewley CA, Clore GM (2000) Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization. J Am Chem Socety 122(25) 6009-6016... 

The efficiency of widely used programs for rigid body minimization of crystal structures was criticized by Gibson and Scheraga. They introduced a new algorithm, based on secant methods (computationally fast methods to compute derivative matrices ) that efficiently calculate the energy gradient with respect to the minimization variables. 

Upon cryo-cooling, the unit cell dimensions of the l-Ppol crystals shrunk 0.6-1 A on each edge (e.g. from a=59.19A to a=58.58 A, from b=62.13 A to b=61.10 A, and from c=l 12.69 A to c=l 11.70 A for the metal soaked crystal). Simple rigid body minimization followed by Powell minimization of the partially refined room temperature structure or the AMoRe solution did not did not drop the R ge below 40 % for either cryo-cooled data set. The structures were then subjected to torsion angle dynamics protocols (48) at several temperatures. Both starting models, with either data set, failed to produce a structure with an Rfree below 39 % for data between 8 and 2 A. In addition, the resulting maps did not look very good. 

E. C. Meng, D. A. GscJiwend, J. ML Blaney, and I. D. Kuntz, Proteins, 17, 266 (1993). Orientatioi Sampling and Rigid Body Minimization in Molecular Docking. 

---