ML visualization tool of python #machine_learning #visualization

Machine learning is used for QSAR in drug discovery. After building the model, analyze its performance is important. One of the ML package for python named ‘scikit-learn’ has many function for model performance metrics. But it does not provide visualization tools. So I make some plot with matplotlib, seaborn aned etc, But few days ago,

Extract chemical information from patent data #pat-informatics #chemoinformatics

As you know, patent informatics is important for drug discovery project. And SureChembl is one of the dataset for chemical structures which are extracted from patent document by OCR. It is worth that it can freely available data source. I surprised that recently google patents provides chemical data too. It seems not fully cover all

Visualize chemical space as a grid #chemoinformatics #rdkit

Visualize chemical space is important for medicinal chemist I think. Recently, Prof. Bajorath group published nice article. URL is below. https://pubs.acs.org/doi/pdf/10.1021/acsomega.9b00595 The author described new approach that combines SARMatrix and Molecular Grid maps. SARMatrics is one of the method for SAR analysis like Free Wilson analysis. I had interest their approach because they uses molecular

Process development of fluorinated-pyrrolidin analogue #memo #organic_chemistry

Here is an interesting article for efficient synthesis of fluorinated pyrrolidin synthesis from pfizer.https://pubs.acs.org/doi/abs/10.1021/acs.oprd.9b00245 Fluorine containing building blocks are often used medicinal chemistry. So efficient synthetic route is very useful for us. Some years ago, I synthesized similar compounds 1-fluoro-2-amino cyclic amine derivatives. I tried to use almost same synthetic scheme described in scheme1. 1)

Useful package for descriptor calculation #chemoinformatics #rdkit

Descriptor calculation is an important task for chemoinfomatics. I often use rdkit to do it. And today I found very useful package for descriptor calculation which name is descriptorus. URL is below. https://github.com/bp-kelley/descriptastorus It is very easy to install the package. Just following command. After did it, I could use the package. By using the

Calculate solvent effect in Psi4 #psi4 #quantumchemistry

Recently I use not only chemoinformatics tools but also quantum chemistry tool, my favorite is Psi4. Psi4 has many options and plug-ins for quantum calculation. Most setting of calculation is vacuum, but it actually true. So considering the solvent around the molecules is important. Can psi4 perform calculation with solvent effect? Yes! PCMSolver is plugin

Do Pharmas need more data for building better model? #memo #medchem

Is ‘AI’ & ‘BidData’ key for success? Recently many pharmaceutical companies are trying to use AI for their drug discovery project acceleration and cost reduction. However sometime it fails because of lack of training data. It is rare that lots of data is available in early drug discovery projects. It is still difficult to build

Machine learning workflow tool for none programmer #memo #machinelearning #dss

I’m on summer vacation. This summer is high temperature and humidity….. So it is tough for me to running. ;-( And now very big typhoon is coming to Japan. Oops… Let’s leave that aside for now. Today I would like to introduce very cool tool for machine learning. Recently we can use many machine learning

Twist and to be square #MedicinalChemistry #memo

MedChem often care about lipophilicity of their own molecule. But it is very important to keep molecular drug like profiles. Spiro cyclic building block and oxetanes are very attractive components for drug discovery. Following articles are interesting for me. The first one is letter about azaspiroheptanes and the second one is about oxetane containing molecules.

Added Notebook Example for psikit #psi4 #RDKit

Some days ago. I updated psikit, added new function, SAPT. The method can calculate inter-intra molecular interaction with psi4. Psikit can call the method very easily. And I added sample notebook in the repository. Following codes are very simple example of SATP for water dimer and FSAPT for phenol dimer. SAPT for water dimer. F-SAPT

Lead Optimization Mapper(LOMAP) for FEP calculation #chemoinformatics #RDKit #Networkx

Free energy perturbation (FEP) is useful method for Computer aid drug design. The method calculates energy difference between several similar molecules. And the system is closed system. To perform the calculation for several molecules. The efficient method of making molecules system is required. I found an interesting article today. The url is below.https://www.ncbi.nlm.nih.gov/pubmed/24072356 The authors