Dear Fleming, while the methods are different, the CDK does have descriptors for some of the properties you mention. Some are based on the 3D structure, but not all.
When it comes to interactions, less so. The CDK does not have a lot of functionality to calculate or map properties onto the molecular surface. I know that J(S)mol can at least visualize properties onto the surface, but not sure what surface properties it can calculate. Others? Egon On Fri, Jul 3, 2020 at 4:55 PM Fleming Kretschmer < fleming.kretsch...@uni-jena.de> wrote: > 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 > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > -- Hi, do you like citation networks? Already 51% of all citations are available <https://i4oc.org/> available for innovative new uses <https://twitter.com/hashtag/acs2ioc>. Join me in asking the American Chemical Society to join the Initiative for Open Citations too <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature, the RSC and many others already did <https://i4oc.org/#publishers>. ----- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen
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