Conformational energy cutoffs

CORINA and ROTATE both offer methods to restrict the number of output conformations. Besides the classification procedures, energy cutoffs can be defined and the number of rotors to be processed can be specified and weighted by the topological position within the molecule. Thus, the conformational space of a molecule can be explored to a degree required by the user. 

Energy gaps of individual energy terms have also been examined [see Eqs. (1) and (2)]. Unless explicitly noted, all results presented below were performed without energy cutoffs that is, all possible non-bonded interactions are included in the total energy. The structural similarity between two protein conformations is expressed as a root mean square deviation (RMSD) between the best overlap of the alpha-carbon (Co) atoms of the two conformations. 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

Figure 5a. An example of a partial energy map, the local relaxed map for the S4 family of conformations. Contours are indicated at 4, 6, and 8 kcal/mol above the global SI minimum, which does not appear on this map. The dashed lines surround the different inter-residue hydrogen bond domains (with a cutoff criterion of 2.05A for the O. .. H distance), with the tic marks on the d hes pointing toward the region where the given hydrogen bond is allowed.

Molecular energies calculated by - computational chemistry methods are fundamental descriptors commonly used in QSAR models moreover, energies are used as cutoff values for the selection of the most important conformation(s). Besides the... 

This is a molecular index defined as —+ total information content based on the number of conformations of a molecule (usually below a cutoff energy value) [Bonchev, 1983] ... 

Conformational invariance means that molecular descriptor values are independent of the conformational changes in molecules. Conformations of molecules are the different atom dispositions in the 3 D space, that is, configurations that flexible molecules can assume without any change to their connectivity. Usually interest in different conformations of a molecule is related to those conformations for which the total energy is relatively close to the minimum energy, that is, within a cutoff energy value of some kcal/mol. 

The same analysis was performed on the Type II defect simulation for each of the three energy minima highlighted in Fig. 5b (i.e.. A, B, and C). These minima are related to the presence of the outward boundary defect (see Fig. 3) the inward boundary defect appears to have little influence on binding. Within sigma of each minimum, all structures below an RMSD cutoff of 0.2 nm were clustered. This resulted in 9,885 structures in 11 clusters for minimum A, 41,203 structures in 23 clusters for minimum B, and 14,710 structures in 9 clusters for minimum C. The central cluster conformations of the clusters with the top three weights calculated for each of the minima are shown in Fig. 7. 

---