Conformational cluster

Fig. 1.5 Medium effects on average log P values for each conformational cluster.

Conversely, in a membrane model, acetylcholine showed mean log P values very similar to those exhibited in water. This was due to the compound remaining in the vicinity of the polar phospholipid heads, but the disappearance of extended forms decreased the average log P value somewhat. This suggests that an anisotropic environment can heavily modify the conformational profile of a solute, thus selecting the conformational clusters more suitable for optimal interactions. In other words, isotropic media select the conformers, whereas anisotropic media select the conformational clusters. The difference in conformational behavior in isotropic versus anisotropic environments can be explained considering that the physicochemical effects induced by an isotropic medium are homogeneously uniform around the solute so that all conformers are equally influenced by them. In contrast, the physicochemical effects induced by an anisotropic medium are not homogeneously distributed and only some conformational clusters can adapt to them. 

An improvement over methods that use a one-dimensional reaction coordinate for locating transition states is to expand the space of relevant reaction coordinates into multiple dimensions. An example of such an approach is the conformational clustering method of Li and Daggett in which the TSE is determined on the basis of structural changes that occur as the protein unfolds.Structural fluctuations are categorized as being local or large scale, and transition state structures are defined as the ensemble of structures... 

Initial applications of torsional dissimilarity measures concentrated on their use in conformational clusterings. Here, all dissimilarity values are calculated for each of the Nf(Nf -l)/2 fragment pairs in a subset of the database comprising the... 

I Docked Conformation Clustering Parameters for analysis command rmstol 1.0 cluster tolerance (Angstroms)... 

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