Japanese summer is very hot and humid most days. It’s not so good for running.It’s important to stay hydrated. I’m keeping my lunch time 5km Running when I work from home. I could…| Is life worth living?
Molecular filter is important for removing unwanted molecules from huge amout of comound dataset. And there are lots of filters are available in these days. For example, PAINS, Role of 5, Role of C…| Is life worth living?
Data preparation is a really important task in the area of data science. In cheminfomratics tasks, we need curate molecules and properties. One of the my favorite package is chembl_structure_pipeline. Because it is easy to install and has well validated pipeline. The package supports structure preparation but doesn’t data preparation. Today I would like toContinue reading "Useful data preparation package for cheminformatics #RDKit #Aurois #cheminformatics"| Is life worth living?
Recently I think relationship between ML and CADD become more closer compared to several years ago. DiffDock is one of the very nice work for interation of cheminformatics and SBDD. It uses diffusi…| Is life worth living?
March is the end of fisical year in most of Japanese company. So I’m busy…. But fortunately I have a time for coding in this weekend. I tested substructure search with RDKit. Substructu…| Is life worth living?
Shape based alignment approach is useful for LBDD which is not available for target protein structure. However there are few OSS to align molecules like OpenEye’s ROCS. Also GPU based tools a…| Is life worth living?
In the cheminformatics area we often use SMILES wich is 1D representation of molecules. But to conduct virtual screening we should prepare molecules from SMILES to 3D structure whith predict proton…| Is life worth living?
Extended-Connectivity Fingerprints(ECFPs) are a type of molecular fingerprint explicitly designed to capture molecular features relevant to molecular activity. They are among the most popular similarity search tools in drug discovery and they are effectively used in a wide variety of applications.| ChemicBook
In RdKit, the method SetProp is used to set an atomic property for the atoms involved in the molecule. This method takes two arguments: the peroperty to set and its value. The idea is simple: Create an rdkit mol object from SMILES string, iterate over the atoms, and set the desired property to a custom value.| ChemicBook