A key aspect in computational chemistry software is the quality of the descriptors used to represent molecules. In many cases, simplistic representations of chemical entities are used in order to increase the speed of calculations. However, these molecular description simplifications may result in incorrect results.
The importance of using accurate descriptors can be seen in the image example, where two compounds (A) show very different transfer free energy (B) for the same atom type (nitro group) due to the changes in the rest of the molecule (carboxyl and amino group positions). This difference in transfer free energy (B, green cell in table) is translated into different hydrophobic profiles or interaction fields (C) and, therefore, different interactions with the receptor1.
Pharmacelera’s 3D interaction fields are generated with high quality molecular descriptors computed with semi-empirical Quantum-Mechanical (QM) methods 2,3,4. These accurate calculations take into account the influence of conformations and model new chemical groups not calculated in empirical databases, better representing the hydrophobic profile of the molecules.
1.- Muñoz-Muriedas et al.,Journal of Computer-Aided Molecular Design, 19, 2005.
2.- Luque et al., Journal of Computer-Aided Molecular Design 13(139), 1999.
3.- Ginex et al., Journal of Computational Chemistry (JCC), January 2016.
4.- Ginex at al., Journal of Molecular Modelling (JMM), June 2016.