Distance geometry applications

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. 

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

Note that although the bounds on the distances satisfy the triangle inequalities, particular choices of distances between these bounds will in general violate them. Therefore, if all distances are chosen within their bounds independently of each other (the method that is used in most applications of distance geometry for NMR strucmre determination), the final distance matrix will contain many violations of the triangle inequalities. The main consequence is a very limited sampling of the conformational space of the embedded structures for very sparse data sets [48,50,51] despite the intrinsic randomness of the tech-... 

Figure 3 Flow of a distance geometry calculation. On the left is shown the development of the data on the right, the operations, d , is the distance between atoms / and j Z. , and Ujj are lower and upper bounds on the distance Z. and ZZj, are the smoothed bounds after application of the triangle inequality is the distance between atom / and the geometric center N is the number of atoms (Mj,) is the metric matrix is the positional vector of atom / 2, is the first eigenvector of (M ,) with eigenvalue Xf,. V , r- , and ate the y-, and -coordinates of atom /. (1-5 correspond to the numbered list on pg. 258.)...

Blumenthal, L. M. Theory and Application of Distance Geometry, Chelsea, New York, 1970. 

Ghose, A. K., Crippen, G. M. The distance geometry approach to modeling receptor sites In Comprehensive Medicinal Chemistry. The Rational Design, Mechanistic Study and Therapeutic Application of Chemical Compounds, Hansch, C.,... 

Blumenthal, L.M. Tlicory am3 Applications of Distance Geometry. Clarendon Press, Oxford, 1953. 

W. Braun, C. Bosch. L. R. Brown, N. Go, and K. Wiithrich, Biochim. Biophys. Acta, 667, 377 (1981). Combined Use of Proton-Proton Overhauser Enhancements and a Distance Geometry Algorithm for Determination of Polypeptide Conformations. Application to Micelle-Bound Glucagon. 

J. de Vlieg, R. M. Scheek, W. F. van Gunsteren, H. J. C. Berendsen, R. Kaptein, and J. Thomason, Proteins, 3, 209 (1988). Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data Application to the DNA Binding Domain of lac Repressor from Escherichia coli. 

In the past, computational chemistry has been considered to be mainly synonymous with quantum chemistry. However, exciting developments of computational chemistry include molecular mechanics and dynamics applications to organic and biological molecules, computer graphics to study the properties of complex molecules, and distance geometry methods.. .. It is clear that a combination [of approaches] is more powerful than each is alone. 

Srivastava, S., Richardson, W.W., Bradley, M.P. and Crippen, G.M. (1993). Three-Dimensional Receptor Modeling Using Distance Geometry and Voronoi Polyhedra. In 3D QSAR in Drug Design. Theory, Methods and Applications. (Kubinyi, H., ed.), ESCOM, Leiden (The Netherlands), pp. 409-430. 

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