checks.rst

Checks

Example failure modes

In molecular conformation generation, docking, and de-novo molecular generation the generated molecules conformation should have a reasonable geometry including standard bond lengths and angles and no steric clash.

Bond lengths
Bottom left carbon-oxygen bond too short

Bond angles
Bond angles off and atoms clashing

Steric clash
Molecule intertwined and atoms clashing

High energy conformation
Twisted rings energetically unfavorable

Aromatic rings not flat
Conjugated pi bond systems should be flat

In docking the molecular identity should be preserved including stereochemistry.

Tetrahedral stereochemistry changed
Top right oxygen facing the wrong way

Double bond stereochemistry changed
Right most double bond should be cis

In de-novo molecular generator or docking the generated molecule should be placed with in a receptor's binding pocket without any steric clash.

Volume overlap
Ligand and receptor clash

More details on tests and docking method comparison

For more detailed information about the tests and for a study using PoseBusters to compare docking methods, refer to our preprint:

@online{buttenschoen2023posebusters,
title = {{{PoseBusters}}: {{AI-based}} Docking Methods Fail to Generate Physically Valid Poses or Generalise to Novel Sequences},
shorttitle = {{{PoseBusters}}},
author = {Buttenschoen, Martin and Morris, Garrett M. and Deane, Charlotte M.},
date = {2023-08-10},
eprint = {2308.05777},
eprinttype = {arxiv}
}