Distance geometry ensemble approach

Sheridan R P, R Ndakantan, J S Dixon and R Venkataraghavan 1986. The Ensemble Approach to Distanc Geometry Application to the Nicotinic Pharmacophore. Journal of Medicinal Chemistry 29 899-906. 

RP Sheridan, R Nilakatan, JS Dixson, R Venkataraghavan. The ensemble approach to distance geometry Application to the nicotinic pharmacophore. J Med Chem 29 899-906, 1986. 

Another useful distance geometry model-building application is the elegant ensemble approach of Sheridan et al. (145), where multiple molecules are entered into a single distance bounds matrix. Intramolecular distance constraints are set as described in Section VII.A and mtermolecular distance constraints are entered to force specific intermolecular interactions to occur, for example, to superimpose a set of molecules using common functional groups. This approach is described in more detail in Section X.B on pharmacophore modeling. 

The ensemble distance geometry pharmacophore modeling approach of Sheridan et al. (145) provides the most direct and efficient method for... 

The Ensemble Approach to Distance Geometry Application to the Nicotinic Pharmacophore. 

By examining the stmctures of the two microcystins as derived from the distance geometry calculations, many of the NOES could not be described using the standard method of applying the NOEs to one conformation. Distance violations approaching 1.0 A were observed, particularly for the residues located around the Mdha residue. The constraint that this residue introduces into the cyclic peptide is significant, and it could very well be the source of dynamics, fast on the NMR time-scale. With this in mind, we undertook the calculation of these two inhibitors of the protein phosphatases 1 and 2A using the ensemble approach. 

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