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 ...
Tyberius's user avatar
  • 15.5k
12 votes
Accepted

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") ...
Geoff Hutchison's user avatar
10 votes
Accepted

Is it possible to calculate the pka value of different H atoms on one molecule?

Yes. Simply calculate the pKa from the definition: $$ \rm{pK_a} = \lg \frac{[AH]}{[A^-][H^+]} \tag{1} $$ The equilibrium constant in the logarithm is computed from the Gibbs free energy of the ...
wzkchem5's user avatar
  • 9,621
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 $R^2$....
Geoff Hutchison's user avatar
7 votes
Accepted

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 <...
Geoff Hutchison's user avatar
5 votes
Accepted

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 ...
Tyberius's user avatar
  • 15.5k
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 ...
Buttonwood's user avatar
  • 1,579
4 votes

Getting interpretable chemical information from hashed molecular fingerprints

I don't know of any simpler methods. Heuristic methods such as Neural Networks are likely your better option if you wish to actually reconstruct the original molecule. Keep in mind that an active bit ...
stanton63's user avatar
  • 124
2 votes
Accepted

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 ...
Roman's user avatar
  • 2,373

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