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 ...
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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 ...
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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 ...
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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
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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&...
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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:
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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 ...
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Difference between bioinformatics and cheminformatics [closed]
Anyone can answer, and should be in simple way
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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 ...
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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 ...
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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 ...
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