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85192504610
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note
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To apply this algorithm, either a "primordial receptor model" or a "van-der-Waals envelope" must be generated beforehand. The former may simply consist of a few key amino-acid residues appropriately positioned in 3-D space while the latter is defined by virtual particles (for example with a radius r=0.8 Å and a well-depth ε = 0.024 kcal/mol) surrounding the ensemble of ligand molecules - an option with PrGen. For receptor models, the interactions are calculated according a the direction force field [23]. For virtual envelopes, the vander-Waals interactions between each ligand and any virtual particle are calculated using a 6-12 potential; the electrostatic field is computed using a partial charge of +1.0 on the virtual particle; H-bond interactions do not exist with a virtual construct. Next, the three classes (electrostatic, vander-Waals, and H-bond interactions) are each mean centered and scaled (to range from -1.0 to +1.0)) - in order to equally weight the different terms. Optionally, the experimental ΔG° might also be included as a parameter contributing to "the minimum distance".
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Böhm, H.-J., The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Design 8, 243-256 (1994).
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Holloway, M.K., Wai, J.M., Halgren, T.A., Fitzgerald, P.M.D., Vacca, J.P., Dorsey, B.D., Levin, R.B., Thompson, W.J., Chen, L.J., deSolms, S.J., Gaffin, N., Gosh, A.K., Giuliani, E.A., Graham, S.L., Guare, J.P., Hungate, R.W., Lyle, T.A., Sanders, W.M., Tucker, T.J., Wiggins, M., Wiscount, C.M., Woltersdorf, O.W., Young, S.D., Darke, P.L. and Zugay, J. A., A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 38, 305-317 (1995).
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85192505324
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note
-
As in a pseudoreceptor context, "n" ligand molecules bind "simultaneously" to an averaged receptor model, the non-bonded list is modified in such a way that each ligand interacts with the pseudoreceptor, but is not affected by any of the other ligand molecules. Moreover, all interactions between pseudoreceptor and ligand atoms are normalized, removing the dependency of the forces experienced by pseudoreceptor atoms from the total number of ligand molecules present in the system.
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34
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85192504617
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note
-
During correlation-coupled refinement, we limit the target RMS deviation to a value corresponding to the experimental error associated with the binding affinities - as the model may not be more accurate than the experimental data it is based on (typically 0.130 or 0.236 kcal/mol, corresponding to uncertainties of 25% and 50% in the experimental binding affinity, respectively).
-
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35
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85192504745
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note
-
During the Monte-Carlo procedure, the position, orientation and conformation of each ligand molecule is typically altered 100-250 times using the Metropolis criterion for accepting or rejecting a new position, orientation and conformation. By default, every tenth structure is minimized retaining that with the lowest total energy for each ligand molecule. The range of the underlying positional, orientational and conformational changes is individually adjusted for each ligand molecule such as to keep the ratio of accepted and rejected positions, orientations and conformations close to unity. To calculate the Boltzman factor for the Metropolis criterion, we typically use a temperature of 10,000 K. Moreover, only those positions, orientations and conformations are accepted which feature a RMS separation of greater than typically 0.5 Å compared to the previously minimized ligand structure. This avoids the reproduction of spatially close positions, orientations and conformations.
-
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36
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85192504839
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note
-
As a result one would expect the (now) predicted free binding energies being close to the ones calculated for the training set. Moreover, position, orientation and conformation of the individual ligand pairs (in the true training set and the "training set treated as a test set", respectively) should be acceptably close - typically less than 0.5 Å (RMS).
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85192504729
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note
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solvation,ligand.
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