Skip to main content
3 votes
Accepted

How can I identify acceptor and donor atoms using BioPython?

A hydrogen bond donor heavy atom is one that is protonated, while the acceptor has a lone pair. If you talking about amino acids, then it's simple as they are fixed. atom name description role note <...
Matteo Ferla's user avatar
  • 4,244
2 votes
Accepted

Why do molecular generation models maximize “penalized logP” as a measure of drug-likeliness?

A positive logP is good (hydrophobic), but high results in ADMET problems (cytochromes break overly hydrophobic compounds) and aggregation (gunk, tar, crud are words happily thrown around). However, ...
Matteo Ferla's user avatar
  • 4,244
1 vote

Why do molecular generation models maximize “penalized logP” as a measure of drug-likeliness?

You were trapped by arXiv versioning convention that shows you the latest version of the preprint as default. It seems that this experiment was removed from the final publication. If you have a look ...
dopexxx's user avatar
  • 111
1 vote

Building small molecules de novo

Most universities have a ChemDraw site lincence, so you may want to check that for drawing a non–3D-embedded molecule. Alternatively there are many other programs. PyMOL is not really a good choice. ...
Matteo Ferla's user avatar
  • 4,244
1 vote

How do I convert an Excel file (.xlsx) to an .smi file format?

So a smi file is simply a text file formatted SMILES tab name newline. Therefore what you need to do is save for safety make a ...
Matteo Ferla's user avatar
  • 4,244

Only top scored, non community-wiki answers of a minimum length are eligible