Molecule auto-correction to facilitate molecular design

2024/02/16 by Alan Kerstjens, Hans De Winter · 1 voice · 4 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Materials Science · Mathematics · #Algorithm #Chemical Synthesis and Analysis #Chemistry #Combinatorics #Computational Drug Discovery Methods #Computer science #Machine Learning in Materials Science #Mathematics #Molecule #Programming language #Set (abstract data type) #Theoretical computer science #Tree (set theory)

paper · pdf · doi:10.1007/s10822-024-00549-1

published in Journal of Computer-Aided Molecular Design 38(1), 10 (Springer Science+Business Media)

openalex publication_date 2024/02/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05

Abstract

Ensuring that computationally designed molecules are chemically reasonable is at best cumbersome. We present a molecule correction algorithm that morphs invalid molecular graphs into structurally related valid analogs. The algorithm is implemented as a tree search, guided by a set of policies to minimize its cost. We showcase how the algorithm can be applied to molecular design, either as a post-processing step or as an integral part of molecule generators.

Citations

• On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other
• Comparing Individual Means in the Analysis of Variance

Cited by

• SMILES all around: structure to SMILES conversion for transition metal complexes
• SMILES all around: structure to SMILES conversion for transition metal complexes. [europepmc]
• C2PO: an ML-powered optimizer of the membrane permeability of cyclic peptides through chemical modification. [europepmc]

Discussions

• Molecule auto‑correction to facilitate molecular design doi.org/10.1007/s108... #compchem [bsky, 39 points, 1 comments]

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