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14 votes

Computational tool for identification of activity cliff

A 2015 paper [1] looked at the ability to predict activity cliffs structurally using docking models that could combine experimental and computational information about the conformation of the receptor ...
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8 votes
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Getting interpretable chemical information from hashed molecular fingerprints

Using RDKit, it's fairly easy to depict bits on example molecules - it's even an example in the documentation "Generating Images of Fingerprint Bits") ...
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7 votes

How to improve my cross-validation R2_score?

You don't give a lot of details (e.g., type of model, target property, etc.), but with only 300 molecules, it's very likely that your model is over-fit. Thus when you cross-validate, you get low $R^2$....
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5 votes
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How are structure descriptors used in regression or machine learning?

One way that matrix information can be passed into a learning algorithm is by diagonalizing it and instead passing in the sorted eigenvalues. An example of this in a fairly recent paper[1] is the use ...
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5 votes

How to input 3D coordinates from xyz file and connectivity from SMILES in rdkit?

Your best bet is to keep the molecule (e.g., as a .mol or .sdf file) around and then simply update the coordinates from the <...
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4 votes

How to input 3D coordinates from xyz file and connectivity from SMILES in rdkit?

The representation of a molecular structure as SMILES string is a (very) reduced one, often with only implicit hydrogen atoms. Recreating a 3D molecular structure with either OpenBabel or RDKit not ...
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2 votes
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Software to generate compound library

Upon the request I'm sharing the solution I came to. So, as I mentioned in the comments, I've finally make MarvinSkectch Markush enumeration feature to work properly. I don't really know what I've ...
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