Questions tagged [qsar]

Quantitative structure–activity relationship (QSAR) is a regression technique to predict the properties, activity, and reactivity of unknown molecules based on molecules where these are known.

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

I like to calculate pka values for two different H atoms in one molecule. Is it possible to do so with computational methods? I have gaussian and orca as software to use. I searched in the internet ...
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10 votes
2 answers
229 views

Getting interpretable chemical information from hashed molecular fingerprints

I have been using molecular fingerprints like ECFP (extended connectivity fingerprint), APFP (atom-pair fingerprint) etc. in my research to predict spectral properties of organic molecules with ...
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6 votes
1 answer
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How to improve my cross-validation R2_score?

I built a prediction model with fingerprints from 300 molecules and got an R2 of 0.9 However when I go to perform a cross-validation I get a very low R2. How can I improve this result? I'm using ...
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9 votes
2 answers
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How to input 3D coordinates from xyz file and connectivity from SMILES in rdkit?

I am working on a QSAR project where the 3D structural descriptors are an input to a machine learning model. I am generating the descriptors using the python Mordred API (which uses rdkit). ...
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13 votes
1 answer
112 views

How are structure descriptors used in regression or machine learning?

I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
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7 votes
1 answer
112 views

Software to generate compound library

I'm trying to perform a QSPR research and for it I need to generate a library of compounds. Now I'm using a plugin for MarvinSkectch for enumerating Markush structures but it doesn't work properly (...
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19 votes
1 answer
125 views

Computational tool for identification of activity cliff

Activity cliffs are defined as pairs of similar compounds with substantial differences in activity (Molecular Diversity, 19, 1021–1035 (2015)). Are there computational tools for the identification of ...
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