Predict protein-ligand complex dynamics with python #dynamicbind #cheminformatics #memo

Computer aided drug design is one of the powerful approach for drug discovery these days. Docking study of target protein and ligands is common proceduer to evaluate whether the compound fit target protein’s pocket or not. However there is a limitation in the method. Most of the docking apporach handle protein and ligand as rigid

Try to use mmpdb v3.1 #RDKit #MMPDB #cheminformatics

As many RDKitters know that Andrew released new version of MMPDB! Recent version of MMPDB has lots of useful methods, one of the generate method it can generate new molecules from given smiles. The method can generate not only all possible molecules from MMPDB but also constrained molecules with options, ‘–query’ and ‘–constant’. ‘–query’ option

Extract format data from chembl with Dask #cheminformatics #memo #chembl

Happy new year. I hope reader had nice year-end holidays. I started running from 1st Jan. I would like to run 1500 km in this year. ast year, I posted about REST api usage of chembl multitask target prediction. It allows predict possible target without any ML env in user PC. But sometime user would

Useful ML package for cheminformatics #RDKit #cheminformatics #ML

As many readers know that scikit-learn is the one of useful python package for cheminformatics. However to use scikitk-learn in cheminformatics tasks user need to prepare data with other packages becuase scikit-learn doesn’t support chemicaldata handling. So is it nice if you can use chemical data in scikitlearn API? I think so. Fortunately there is