Questions tagged [cheminformatics]

Cheminformatics is the computational analysis and enumeration of small molecules

Filter by
Sorted by
Tagged with
1 vote
0 answers
16 views

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 ...
user avatar
  • 11
1 vote
0 answers
8 views

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 ...
user avatar
  • 159
0 votes
0 answers
11 views

How to generate chemical picture from SMILES code with OPEN Babel?

I would like to generate a chemical picture of some nucleosides from their SMILES code. I found this fancy generator on the internet. The layout is of course based on OpenBabel. I would like to know ...
user avatar
1 vote
1 answer
38 views

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&...
user avatar
  • 133
1 vote
1 answer
247 views

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: ...
user avatar
-1 votes
1 answer
41 views

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 ...
user avatar
  • 29
2 votes
1 answer
132 views

Difference between bioinformatics and cheminformatics [closed]

Anyone can answer, and should be in simple way
user avatar
  • 29
0 votes
1 answer
60 views

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 ...
user avatar
1 vote
0 answers
96 views

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 ...
user avatar
0 votes
1 answer
319 views

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 ...
user avatar