Questions tagged [cheminformatics]

Cheminformatics is the computational analysis and enumeration of small molecules

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Sql query slow on Chembl postgres database

Doing complex sql query on Chembl database and it takes 40 minutes on the machine from lab. I was thinking using dask, extract each table and export to parquet, when do the data processing . Is this a ...
Jack2501's user avatar
3 votes
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How to select the best ligands in a virtual screening matrix

I have the results of a virtual screening experiment using docking simulations with Autodock Vina. The result is a matrix of 7 (proteins) by 28000 (ligands) with the calculated binding energies for ...
albertr's user avatar
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Good molecular docking software?

I'm looking for some good molecular docking software (preferably, one that comes with a Python API). I obviously found Vina and that's been quite helpful but I was wondering if there's anything out ...
apvn's user avatar
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Drug indication data for only cancer phenotype from Chembl

I am interested in getting the drug indication data for all drugs in the database using sqlite. I used following step to get this ...
Megha's user avatar
  • 395
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1 answer

Complete List of IUPAC Chemical Naming Conventions for Formal and Trivial Names?

Two-parted question: Where is a cheatsheet or complete list of the "formal" IUPAC naming conventions? Where is a cheatsheet or complete list of the "trivial" or "informal&...
Lance's user avatar
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How to convert amino acid sequence to SMILES format

I have an amino acids string "MKGK" and I would like to convert it into SMILES format. I tried two approaches. First with PepSMI which gives me: ...
littleworth's user avatar
-1 votes
1 answer

general cheminformatics references

Can anyone explain what is cheminformatics and how does it help in the future? I need to write an article that should be understandable for 14-20 yr age group. Please help with references, I don't ...
Harsha's user avatar
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2 votes
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Difference between bioinformatics and cheminformatics [closed]

Anyone can answer, and should be in simple way
Harsha's user avatar
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1 vote
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Do you know any virtual screening libraries with small, soluble compounds?

I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
Sherbert184's user avatar
1 vote
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Question about Using MDAPackmol (packmol in python)

I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on GitHub so I can gain an ...
bioinf99's user avatar
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How do I convert an Excel file (.xlsx) to an .smi file format?

How do I convert an Excel file(.xlsx) to .smi file format? The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
Shahbaaz's user avatar