Lightning talk at 2023 RDKit UGM.  Describes work on loading PDB files into RDKit using cif templates to assign bond orders

Gowers, Richard J.

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 https://openfree.energy/ OpenFree EnergyPDBinf: A rules based system for nonstandard amino acid and nucleotide recognition in RDKit         Problem statementLoading proteins/biopolymers into rdkit sort of works, except for nonstandard amino acids etc.Having “cheminformatically correct” representations is important for analysis, but also the next generation of force fields, which are using SMARTS patterns to assign parameters.E.g. if I want to assign force field parameters to a PTM.         PDBinf for bond order assignmentPDBinf is a little package for reading PDB(x) files, and trying to apply extra information from monomer templates to build cheminformatically-accurate models.This can handle standard amino acids/RNA/DNA… And also all of the nonstandard residues in the PDB chemical component dictionary (CCD).Templates come from this PDB CCD.  The dynamic nature of the CCD make it unsuitable for the current “compile everything” approach.         MolHash for amino acid lookupEach monomer (residue) in the biopolymer is assigned a residue name.  These names are used to lookup the correct template.It is however traditional to mislabel things in PDB files.rdMolHash with element graphs turns a nasty graph matching problem into an easy string lookup problem.See:https://www.nextmovesoftware.com/talks/OBoyle_MolHash_ACS_201908.pdf         SMARTS lookup to assign atom namesWithin a residue, each atom has a unique name, occasionally these are very useful.Again these are often mislabelled, making some things more difficult than they should be.SMARTS w/ atom mapping can allow you to rename atoms to their canonical names.         ConclusionPDBinf is a hacky package for loading PDB(x) files into RDKit that I’ve put together.It can:● Load data from PDB(x) files into rdkit (with bonds assigned from templates, not guessed from geometry)● Figure out what your mislabelled residues are.● Figure out what your atom names should be.https://github.com/OpenFreeEnergy/pdbinfXyz2mol module serves a similar function, but in contrast:- Is a stack of heuristics so will work without templates- Rules based system offers different tradeoff in precision vs recall

PDBinf: A rules based system for nonstandard amino acid and nucleotide recognition in RDKit

https://zenodo.org/record/8369849/files/Gowers_Lightning.pdf

PDBinf: A rules based system for nonstandard amino acid and nucleotide recognition in RDKit

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