mol2graph and graph2mol #rdkit #igraph

I posted about mol to graph object before. In the blog post, I wrote example that convert RDKit mol object to igraph object. It was one way. There was no method igraph to rdkit mol object. So I wrote very simple converter from graph to molecule. First, import modules. Then define two way function, mol2graphContinue reading “mol2graph and graph2mol #rdkit #igraph”

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Make Drug central ER diagram with python #chemoinfo

Recently I knew useful database “DrugCentral“. From About. DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. We monitor FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. By using the site, user can search many information on webContinue reading “Make Drug central ER diagram with python #chemoinfo”

GCAPS-CNN

Graph convolution neural network (GCN) is useful for chemoinfo because molecules can be represent as graph structure. But GCN approach in chemoinfo has difficulties that each graph has different structure compared to image data. There are many reports about applying GCN for chemoinfo. Sometime GCN approach outperforms other method such as CNN with molecular fingerprint.Continue reading “GCAPS-CNN”

Think about Structure Kinetics Relationship

Here is a deep analysis about SKR from Merck. https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.8b00080 Recently it is becoming important factor for understanding ligand target binding kinetics. You know there are tools such as SPR, ITC and in silico method like a MD. The author analyzed Kinetic data about Hsp90. They analyzed relation ship between R-group of some scaffolds andContinue reading “Think about Structure Kinetics Relationship”

Make MMP network and send to cytoscape #chemoinfo

Recently I use cytoscape in my laboratory. You know Cytoscape is nice tool for network visualization. I often make data with python and import data from cytoscape. The work flow is not so bad but I am thinking that it will be nice if python can communicate with cytoscape. Fortunately cytocape has REST plugin calledContinue reading “Make MMP network and send to cytoscape #chemoinfo”