Conformal prediction with python and rdkit_2 #RDKit #QSAR #Conformal_prediction

I posted about conformal prediction with python and rdkit some days ago. After that I could get very informative advice from @kjelljorner. Thanks a lot! His advice was below. Kjell Jorner @kjelljorner3dReplying to @iwatobipen I can recommend the cross conformal prediction or bootstrapped conformal prediction (also in nonconformist) to avoid having to put aside data for calibration.Continue reading “Conformal prediction with python and rdkit_2 #RDKit #QSAR #Conformal_prediction”

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Conformal prediction with python and rdkit #RDKit #QSAR #Conformal_prediction

Recently Greg shared nice webiner about conformal prediction in Youtube. https://www.youtube.com/watch?v=_ZVuEWEfwuw He introduced basic concept of conformal prediction and demonstration with excellent work flow of KNIME. I recommend to check the site. ;) Conformal prediction is not new method. It can estimate confidence of predicted values. Traditional predictive model can predict probability, or class ofContinue reading “Conformal prediction with python and rdkit #RDKit #QSAR #Conformal_prediction”

Deep learning based reaction mapper #rdkit #deeplearning #AAM #chemoinformatics

Here is a great article about AtomAtom Mapping with Deep Learning!https://chemrxiv.org/articles/Unsupervised_Attention-Guided_Atom-Mapping/12298559The author use attention method and train model for reaction mapping. AAM is important technology but there are few tools to do it. The author shared their code! Thanks. I have interest the code. So I installed the code and used the package. Following codeContinue reading “Deep learning based reaction mapper #rdkit #deeplearning #AAM #chemoinformatics”

Think about de novo molecule generation #memo #journal #RDKit #CReM

Recently there are many publications about de-novo molecular generator which mainly use Deep Learning. One problem of the approach is that generated molecules are not systematic so it’s difficult to synthesis them with parallel chemistry. So sometime chemists dislike the proposal from generated form the method I think. Rule or Rxn or MMP based moleculeContinue reading “Think about de novo molecule generation #memo #journal #RDKit #CReM”

Molecules drawing code memo (Highlight Functional groups) #memo

Here is an example for draw molecules with FG highlighting. Improved version of the code can be found in last part of the post. RDKit has fdef file for common functional groups. So we can use it for highlighting atoms as same as pharmacohore. Today’s example is just for my memo. Because I often forgetContinue reading “Molecules drawing code memo (Highlight Functional groups) #memo”

Replace core with DeLinker #RDKit #Chemoinformatics #DeepLearning

In the FBDD projects, fragment linking strategy is very easy to understand about the strategy but it is difficult to linking two fragments in the real world I think. There are many tools for linking fragments in virtually. These tools are used not only be applied to FBDD but also scaffold hopping etc. There areContinue reading “Replace core with DeLinker #RDKit #Chemoinformatics #DeepLearning”

Compare the view point of different QSAR models #RDKit #visualize #chemoinformatics

Some days ago, I posted how to visualize SVG images horizontally and ngboost for QSAR problem. It worked well. And I found that different models showed different performance. So my question is that which point each model detects important for molecular properties. Fortunately rdkit has GetSimilarityMapForModel method which can render the probe molecule with model’sContinue reading “Compare the view point of different QSAR models #RDKit #visualize #chemoinformatics”

Try to use target DB #OSS #targetDB #memo

I posted the article about CADD for drug discovery today. And in the article, author introduced many useful CADD tools and targetDB is one of them. Reader who would like to install it, pip or conda command is available.https://github.com/sdecesco/targetDB I installed targetdb with pip because conda caused error during the instllation. After installing the packageContinue reading “Try to use target DB #OSS #targetDB #memo”

Computer supports drug discovery #memo #journal

In this week is called ‘Golden week’ in Japan, which is a collection of national holidays. Due to fight against new corona-virus, I spend most of time in my home and around my home with my family. And in this morning I read a miniperspective in JMC. The title was ‘Computational Chemistry on a Budget:Continue reading “Computer supports drug discovery #memo #journal”

Predict probabilistic distribution with NGBoost #NGBoost #RDKit #QSAR #Chemoinformatics

Recently novel gradient boosting method was published from Andrew Ng group. It is interesting that NGBoost can calculate not only probability but also probabilistic distribution. It is useful for QSAR because we would like to know not only predicted value/class but also uncertainly of the prediction. Fortunately NGBoost is available from python! It can beContinue reading “Predict probabilistic distribution with NGBoost #NGBoost #RDKit #QSAR #Chemoinformatics”

Draw molecules as SVG in horizontal layout #Drawing #RDKit #memo

As you know, Greg posted cool code about new drawing code options of rdkit 202003. You can read details of them in following URLhttp://rdkit.blogspot.com/2020/04/new-drawing-options-in-202003-release.html It’s really cool! New version of rdkit can render molecule with many options in high quarity. In the post, molecules are rendered as SVG image one molecule per one cell. IContinue reading “Draw molecules as SVG in horizontal layout #Drawing #RDKit #memo”