Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Investigating 3D Atomic Environments for Enhanced QSAR   Predicting bioactivity and physical properties of molecules is a longstanding
challenge in drug design. Most approaches use molecular descriptors based on a
2D representation of molecules as a graph of atoms and bonds, abstracting away
the molecular shape. A difficulty in accounting for 3D shape is in designing
molecular descriptors can precisely capture molecular shape while remaining
invariant to rotations/translations. We describe a novel alignment-free 3D QSAR
method using Smooth Overlap of Atomic Positions (SOAP), a well-established
formalism developed for interpolating potential energy surfaces. We show that
this approach rigorously describes local 3D atomic environments to compare
molecular shapes in a principled manner. This method performs competitively
with traditional fingerprint-based approaches as well as state-of-the-art graph
neural networks on pIC$_{50}$ ligand-binding prediction in both random and
scaffold split scenarios. We illustrate the utility of SOAP descriptors by
showing that its inclusion in ensembling diverse representations statistically
improves performance, demonstrating that incorporating 3D atomic environments
could lead to enhanced QSAR for cheminformatics.

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The categories of this paper are: hep-th
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The categories of this paper are: acc-phys
21
The categories of this paper are: adap-org
15
The categories of this paper are: nucl-ex
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The categories of this paper are: stat
8
The categories of this paper are: hep-ex
26
The categories of this paper are: bayes-an
18
The categories of this paper are: econ
31
The categories of this paper are: ao-sci
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The categories of this paper are: astro-ph
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The categories of this paper are: q-fin
37
The categories of this paper are: supr-con
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The categories of this paper are: math-ph
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The categories of this paper are: math
0
The categories of this paper are: hep-ph
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The categories of this paper are: quant-ph