Site-based predictive methods

Various predictive methods based on molecular graphs of Jt-systems as described in Section 3 have been critically compared by Klein (Klein et al., 1989) and can be extended to more quantitative treatments. In principle, the effective exchange integrals /ab in the Heisenberg Hamiltonian (4) for the interaction of localized electron spins at sites a and b are calculated as the difference in energies of the high-spin and low-spin states. It was Hoffmann who first tried to calculate the dependence of the M—L—M bond... 

Ensemble Catalyticphore based docking and activation energy estimation model N = 45 substrates for CYP3A4. N = 25 substrates for CYP3A4. 77.8-81.9% of metabolic sites correctly predicted using a combination of structure based method and activation energy estimation. 203... 

Dai T, Liu Q, Gao J, Cao Z, Zhu R (2011) A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. BMC Bioinformatics, 12(Suppl 14) 9... 

Zhang N, Li B-Q, Gao S, Ruan J-S, Cai Y-D (2012) Computational prediction and analysis of protein [gamma]-carboxylation sites based on a random forest method. Mol Bio Syst 8 2946-2955... 

Recently, a novel decomposition-based approach has been proposed for predicting binding site structures in the MHC 11 HLA-DRl protein [183]. In this approach, existing MHC n crystal structures are used to predict the binding site conformations of other MHC n molecules. The approach uses the detailed potential energy force field ECEPP/3 and an area-based solvation method. A... 

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