Install rdkit to CentOS7

I use OSX or unbuntu for coding usually. But, some case CentOS is needed to make some services. So, I checked the way to install rdkit to centos7. I used docker for my test, because docker can make virtual environment in my mac book. First I pull the Cent OS ver7. Then run the image.Continue reading “Install rdkit to CentOS7”

Visualize chemical space using Knime rdkit node

Usually I use python for analyse, visualize chemical space. Because, I love coding. ;-) I know, work flow tool is useful solution to do that. So, I tried to plot chemical space using Knime. Knime is one of famous work flow tool and lots of nodes are developed. I made very simple work flow toContinue reading “Visualize chemical space using Knime rdkit node”

Scoring 3D diversity using RDKit #RDKit

Recently importance of 3D character of molecules are increasing. If I design a libraries, I want to estimate not only 2D, but also 3D diversity. Fortunately RDKit implemented function for characterize the 3D character of molecules named ‘plane of best fit’ (PBF). You can call this function from rdkit/Contrib/PBF folder. ;-) Great!!! And reference ofContinue reading “Scoring 3D diversity using RDKit #RDKit”

Make virtual machine for chemoinformatics #RDKit

Recently stable version of docker for mac is released. It’s good news for me. ;-) I used boot2docker before but, now I switched docker for mac. Because it’s easy to install and share the file with host OS. Of course, I installed docker for mac ! Virtual machine is one of useful way toContinue reading “Make virtual machine for chemoinformatics #RDKit”

Make polar plots of exit vector about di-amine molecules #RDKit

I posted blog about compare exit vector distance of two molecules some days ago. I used cartesian system to calculate distance of two molecules before. Today I tried to make polar plot using RDKit and matplotlib. ;-) I used 3d amine dataset and made my old code. At first I make scatter plot of similarityContinue reading “Make polar plots of exit vector about di-amine molecules #RDKit”

Natural Product likenes Score

Some years ago, large amount of molecules produced by using palladium catalysed cross coupling reaction, like suzuki-miyaura, negishi, stille, etc. It showed great impact for medicinal chemistry but these reaction tend to produce flat molecules like low fsp3 score. Now I often read the word ‘Escape from flat land, sp3 rich molecules, 3D diversity …’.Continue reading “Natural Product likenes Score”

plot data using RDKit-PandasTools

I often use SDMolSupplier method to read SDF. But, PandasTool is another useful way to read SDF. But, to handle property data, I need to convert data to float. Today I read a major supplier’s SDF. And plot data using seaborn. Fig 3 indicates that the dataset have many FSp3 rich molecules. I’m interested inContinue reading “plot data using RDKit-PandasTools”

calculate exit vector distance of each molecule v2.

Somedays ago, I posted the topics about ‘exit vector’. The way to represent chemical space give me new insight for molecular design. I think it’s useful for replacement of linkage or scaffold. It’s important for drug discovery to design new molecules that similar ligand for target, but not similar for competitor’s one. So, I addedContinue reading “calculate exit vector distance of each molecule v2.”

Predict residence time using MD

I’m not so interested in MD but some days ago I found attractive research of MD. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein–Ligand Residence Times I was interested in the article because, residence times are important for drug discovery, it’s related not only in vivo efficacy but also cell activity.Continue reading “Predict residence time using MD”