Questions tagged [cheminformatics]

Synonym for chemoinformatics. For questions about applying informatics techniques to study chemical systems.

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12 votes
3 answers
2k views

Artificial intelligence is a hot topic, but should I pursue it if I'm interested in Matter Modeling?

Since my previous question seems to have a large number of views, I would like to ask my central question. I am a student now and should decide my major to research soon. AI/ML is a very hot research ...
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5 votes
1 answer
74 views

What is the best way to measure similarity between molecules of the same formula?

I have enumerated a large set of carbocations all of the formula C10H17+, all of course with differing structures. I know there are many different approaches of computing similarity between molecules, ...
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5 votes
0 answers
49 views

How to get hydrogen indices in RDKit substructure matches

I am searching for functional groups in RDKit molecules and want to get the corresponding atom indices. Using GetSubstructMatches() however does not return some (...
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10 votes
2 answers
227 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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14 votes
1 answer
659 views

How to start a Machine Learning project for chemical properties prediction?

I know that is a very general question but I would like to start a ML project in Python to predict some chemical properties with a large set of experimental data. The compounds I would like to study ...
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9 votes
0 answers
53 views

Graph Classification via Random Forest

I’m a medicinal chemistry undergraduate student who is preparing his dissertation. My idea would be to create a classifier that can distinguish anticancer drugs as active or inactive and distinguish ...
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8 votes
1 answer
628 views

How to compute the synthetic accessibility score in Python?

I come from a mainly computer science background, but have become involved in a project related to artificial intelligence-based drug discovery. I made a model that generates novel molecules, for ...
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7 votes
1 answer
293 views

How to create molecule image similar with molconvert using RDKit

I have the following molecule in SMILE format (saved as my_molecule.smi): ...
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  • 1,542
8 votes
1 answer
430 views

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
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  • 3,706
8 votes
1 answer
462 views

Functional group detection for group contribution methods

I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each. A similar question was asked on matter modelling specifically for xyz files. ...
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  • 4,066
10 votes
2 answers
1k views

RDkit: While converting a *.sdf file to fingerprint, I'm facing several errors

suppl = Chem.SDMolSupplier('1.sdf') for mol in suppl: if mol is None: continue # print(mol.GetNumAtoms()) fps = [Chem.RDKFingerprint(x) for x in supply] I am ...
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17 votes
6 answers
411 views

What are the applications of chemical graph theory?

Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....
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15 votes
2 answers
427 views

What are the best fingerprints to characterize molecules?

When working with libraries of thousand of molecules or with de novo design (using combinatorial chemistry), it is usual to filter the libraries using as a criterion the molecular similarity. The ...
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15 votes
1 answer
108 views

Types of Discrete molecular models

It is often assumed in cheminformatics that molecules with similar physical structure tend to have similar chemical properties [1]. Based on this, our group has used discrete graphs as a model for the ...
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