Dear all, We're looking for methods to encode the 3D-Structure of molecules and have come across the "VolSurf+" descriptors, used for example in the publication https://doi.org/10.1016/j.aca.2016.02.014 :
"[We use] VolSurf + version 1.7.0.l [28]. This software uses GRID force fields [29] to characterise molecular interactions, such as hydrophilic/hydrophobic and hydrogen bonding donor/acceptor surface volumes around the molecules, using a water probe (OH2), a hydrophobic probe (DRY), a hydrogen-bonding acceptor carbonyl oxygen probe (O), and a hydrogen-bonding donor amide nitrogen probe (N1). Energy maps, called Molecular Interaction Fields (MIFs), were then converted into molecular descriptors. VolSurf + generates 128 molecular descriptors related to molecular shape, volume, polarisability, polar surface area, hydrophobic surface area, lipophilicity, molecular diffusion, and solubility. It also includes specific descriptors, which refer to the volume and relative position of MIFs at given energy values." Does anyone know whether there is a way to do similar computations with CDK or more generally a similar open-source method? Best regards and thanks, Fleming Kretschmer _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
