ArticleJournal of chemical information and modeling2026
Assessing Molecular Contacts Using Atom Environments Described by Ranked Lists.
Article in Journal of chemical information and modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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6 authors.
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Abstract
We investigate the representation of atomic molecular environments as a list of the atoms neighboring an origin ranked by distance. We show that contact densities collected for origin-neighbor pairs of set types have regular and specific distributions when stratified by ranks. This is used to build a scoring function assessing the fitness of individual atoms with respect to their environment (FS, fitness score), as well as to characterize the contact preferences (CP) for pairs of atoms. Tested against the 3DRobot data set, the FS score was found to be highly discriminative of decoys vs native X-ray. The code is freely available on GitHub (https://github.com/DreanoLoic/Fitness_score.git).
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