Surface complementarity

The surface complementarity between the quantum activated complex and the catalytic surrounding media is the main idea of the present theory. The oscillating stereochemical control of the synthesis of thermoplastic elastomeric polypropylene recently reported by Coates and Waymouth [208] can be easily interpreted in terms of catalyst changing surface complementarity. Hill and Zhang have discovered a molecular catalyst that experiences a kinetic and thermodynamic drive for its own reassembly and repair under conditions of catalysis [209]. This is basically what an enzyme does when moving from the apo-structure towards the catalytically apt conformation. 

Wintner, F.A., Moallemi, C.C. Quantized surface complementarity diversity (QSCD) a model based on small molecule-target complementarity. J. Med. Chem. 2000, 43, 1993-2006. 

Protein-Protein Recognition Based on Surface Complementarity. 

Sobolev, V., Wade, R. Vriend, G., and Edeman, M. Molecular Docking Using Surface Complementarity. PROTEINS Structure, Function and Genetics, 1996,25,120-1 29. 

Unreasonable docked binding mode. Fast docking tools cannot produce reliable solutions for all compounds often, even some well-scoring compounds are simply docked to the outer surface of the protein or adopt rather strained conformations to achieve good surface complementarity within the binding pocket. Computational filters help to detect such situations (329). 

Two molecules of complex structure may form a stable complex only when those parts that are important for the binding can come into close contact. From the point of view of the molecular surfaces, this means that both surfaces have to be complementary to some extent in the binding area. This surface complementarity can be identified in simple cases just by inspection of the computer-generated images, although this technique is not very useful for systematic searches. To achieve the latter, a formal classification is necessary. Several methods for the characterization of surfaces in topological terms have been proposed.Mezey and co-workers have established a method for topological analysis of contour... 

Maximal surface complementarity between two molecules is reached when O g is maximal while V g takes a minimum value. The new technology has been tested in an initial application by matching the surfaces of the two flexible proteins tryspin and PTI. In this application the membership functions and x,y were calculated from molecular dynamic simulations similar to those reported earlier. It turns out that the structure of the trypin-PTI complex is very close to that which was found in x-ray studies. 

More recent experience, coming from a wide variety of sources, shows that for acceptable affinity the hydrophobic interactions have to be maintained and good surface complementarity is essential (no holes), but it is not a requirement that all possible hydrogen bonds are made to Gly216 and Aspl89. 

V. Sobolev, R. C. Wade, G. Vriend, and M. Edelman. Molecular docking using surface complementarity. 

---