Install ChEMBL28 & rdkit cartridge #chemoinformatics #RDKit

Recently ChEMBL 28 was released. It’s good news for chemoinformaticitan and time to update your chembldb ;) Of course I did it. At first I tried to build postgresql chembl28 on my main conda env but it was difficult to install rdkit-postgresql due to some package confliction. So I made clean environment for postgresql/rdkit andContinue reading “Install ChEMBL28 & rdkit cartridge #chemoinformatics #RDKit”

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Which is better Graph based or descriptor based model for QSAR prediction? #journal #memo #chemoinformatics

There are lots of Graph convolutional network(GCN) models are applied for QSAR tasks instead of traditional descriptor based model. The interesting point of GCN is that we don’t need feature engineering I think. It means that during the learning process, GCN learns molecular feature from given molecular graph. On the other side, descriptor based modelContinue reading “Which is better Graph based or descriptor based model for QSAR prediction? #journal #memo #chemoinformatics”

Conformer energy minimization with Openforcefield #OpenFF #RDKit

Last month, I posted topics about conformer generation code with rdkit. https://iwatobipen.wordpress.com/2021/01/31/generate-conformers-script-with-rdkit-rdkit-chemoinformatics/https://github.com/iwatobipen/rdk_confgen RDK_confgen can generate multiple conformers from molfile. This code generates conformers with MMFF94s forcefield. On the other hand recently open force field is very attractive package for these are I think. Fortunately OpenFF provides example code for conformer energy minimization as CLI tool.Continue reading “Conformer energy minimization with Openforcefield #OpenFF #RDKit”