Active site prediction

Fig. 5.1 Classification of known active site prediction methods...

Every active site predicted using any software should be validated through docking to know its binding efficiency. 

A Practice Tutorial for Active Site Prediction Using MOE... 

Free Online Tools for Active Site Prediction... 

Molecular volumes are usually computed by a nonquantum mechanical method, which integrates the area inside a van der Waals or Connolly surface of some sort. Alternatively, molecular volume can be determined by choosing an isosurface of the electron density and determining the volume inside of that surface. Thus, one could find the isosurface that contains a certain percentage of the electron density. These properties are important due to their relationship to certain applications, such as determining whether a molecule will fit in the active site of an enzyme, predicting liquid densities, and determining the cavity size for solvation calculations. 

Molecular simulation techniques can be used to predict how a compound will interact with a particular active site of a biological molecule. This is still not trivial because the molecular orientation must be considered along with whether the active site shifts geometry as it approaches. 

Specificity for a particular charged substrate can be engineered into an enzyme by replacement of residues within the enzyme-active site to achieve electrostatic complementarity between the enzyme and substrate (75). Protein engineering, when coupled with detailed stmctural information, is a powerful technique that can be used to alter the catalytic activity of an enzyme in a predictable fashion. 

We have described a general relationship between structure and function for the a/p-barrel structures. They all have the active site at the same position with respect to their common structure in spite of having different functions as well as different amino acid sequences. We can now ask if similar relationships also occur for the open a/p-sheet structures in spite of their much greater variation in structure. Can the position of the active sites be predicted from the structures of many open-sheet a/p proteins ... 

In this structure the loop regions adjacent to the switch point do not provide a binding crevice for the substrate but instead accommodate the active-site zinc atom. The essential point here is that this zinc atom and the active site are in the predicted position outside the switch point for the four central parallel p strands, even though these p strands are only a small part of the total structure. This sort of arrangement, in which an active site formed from parallel p strands is flanked by antiparallel p strands, has been found in a number of other a/p proteins with mixed p sheets. 

Zvelebil, M.J., et al. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. /. Mol. Biol. 195 957-961, 1987. 

Orlova et al. (2003) theoretically studied the mechanism of the firefly bioluminescence reaction on the basis of the hybrid density functional theory. According to their conclusion, changes in the color of light emission by rotating the two rings on the 2-2 axis is unlikely, whereas the participation of the enol-forms of oxyluciferin in bioluminescence is plausible but not essential to explain the multicolor emission. They predicted that the color of the bioluminescence depends on the polarization of the oxyluciferin molecule (at its OH and O-termini) in the microenvironment of the luciferase active site the... 

This paper surveys the field of methanation from fundamentals through commercial application. Thermodynamic data are used to predict the effects of temperature, pressure, number of equilibrium reaction stages, and feed composition on methane yield. Mechanisms and proposed kinetic equations are reviewed. These equations cannot prove any one mechanism however, they give insight on relative catalyst activity and rate-controlling steps. Derivation of kinetic equations from the temperature profile in an adiabatic flow system is illustrated. Various catalysts and their preparation are discussed. Nickel seems best nickel catalysts apparently have active sites with AF 3 kcal which accounts for observed poisoning by sulfur and steam. Carbon laydown is thermodynamically possible in a methanator, but it can be avoided kinetically by proper catalyst selection. Proposed commercial methanation systems are reviewed. 

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