Molecular Interaction Fields: Applications in Drug Discovery by Gabriele Cruciani, Raimund Mannhold, Hugo Kubinyi, Gerd

By Gabriele Cruciani, Raimund Mannhold, Hugo Kubinyi, Gerd Folkers

This distinctive reference resource, edited by way of the world's most precious specialist on molecular interplay box software program, covers all appropriate ideas of the GRID strength box and its functions in medicinal chemistry. complete chapters on 3D-QSAR, pharmacophore searches, docking experiences, metabolism predictions and protein selectivity reports, between others, supply a concise evaluate of this rising box. As an extra bonus, this instruction manual incorporates a CD-ROM with the most recent advertisement models of the GRID application and similar software program.

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Additional resources for Molecular Interaction Fields: Applications in Drug Discovery and ADME Prediction, Volume 27

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A set of 23 WW domains was used to build the 3D-QSAR models, including WW domains that recognise tyrosine-containing peptides, as well as WW domains that can be considered representative of nonbinders’ to tyrosine-containing peptides. 3D-QSAR models were made with both the GRID/GOLPE combination (GRID used for computing MIFs and GOLPE [42] used for chemometric analysis) and with CoMFA (with computation of MIFs and chemometric analysis as implemented in SYBYL (Tripos)). For the GRID/GOLPE model, several probes (CH3, DRY, H, PO4 and combinations of these) were tested.

To account for the dielectrically discontinuous boundary between molecules and the implicit solvent, the method of images may be used (as in GRID), or the Poisson(–Boltzmann) equation solved. The method of images treats the dielectric boundary as an infinite plane whose effect can be modelled by the addition of image charges. Computation of the electrostatic energy using the method of images requires estimation of the depths of the atoms in the target. In GRID, this is done by counting the number of neighboring target atoms within a specified distance and translating this into a depth using a precalibrated scale [2].

9 were generated by the N3+ cationic amine probe which makes good hydrogen bonds to the (red) carboxy oxygen atoms of the target. 9 Conclusions both the interacting atoms are charged, and can therefore make a particularly strong hydrogen bond to each other. GRID also takes account of the local dielectric, and the electrostatic attraction between the target’s oxygens and the cationic probe is therefore attenuated towards the right of the figure, because this is where the probe would be most exposed to the higher dielectric of the surrounding bulk water.

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