Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Generating 3D Molecular Structures Conditional on a Receptor Binding
  Site with Deep Generative Models   Deep generative models have been applied with increasing success to the
generation of two dimensional molecules as SMILES strings and molecular graphs.
In this work we describe for the first time a deep generative model that can
generate 3D molecular structures conditioned on a three-dimensional (3D)
binding pocket. Using convolutional neural networks, we encode atomic density
grids into separate receptor and ligand latent spaces. The ligand latent space
is variational to support sampling of new molecules. A decoder network
generates atomic densities of novel ligands conditioned on the receptor.
Discrete atoms are then fit to these continuous densities to create molecular
structures. We show that valid and unique molecules can be readily sampled from
the variational latent space defined by a reference `seed' structure and
generated structures have reasonable interactions with the binding site. As
structures are sampled farther in latent space from the seed structure, the
novelty of the generated structures increases, but the predicted binding
affinity decreases. Overall, we demonstrate the feasibility of conditional 3D
molecular structure generation and provide a starting point for methods that
also explicitly optimize for desired molecular properties, such as high binding
affinity.

13
The categories of this paper are: quant-ph
24
The categories of this paper are: dg-ga
9
The categories of this paper are: nlin
7
The categories of this paper are: hep-th
8
The categories of this paper are: hep-ex
34
The categories of this paper are: chem-ph
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The categories of this paper are: eess
29
The categories of this paper are: funct-an
5
The categories of this paper are: gr-qc
14
The categories of this paper are: math-ph
15
The categories of this paper are: nucl-ex
2
The categories of this paper are: math
37
The categories of this paper are: supr-con
12
The categories of this paper are: nucl-th
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The categories of this paper are: chao-dyn
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The categories of this paper are: cmp-lg