Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: AI-Bind: Improving Binding Predictions for Novel Protein Targets and
  Ligands   Identifying novel drug-target interactions (DTI) is a critical and rate
limiting step in drug discovery. While deep learning models have been proposed
to accelerate the identification process, we show that state-of-the-art models
fail to generalize to novel (i.e., never-before-seen) structures. We first
unveil the mechanisms responsible for this shortcoming, demonstrating how
models rely on shortcuts that leverage the topology of the protein-ligand
bipartite network, rather than learning the node features. Then, we introduce
AI-Bind, a pipeline that combines network-based sampling strategies with
unsupervised pre-training, allowing us to limit the annotation imbalance and
improve binding predictions for novel proteins and ligands. We illustrate the
value of AI-Bind by predicting drugs and natural compounds with binding
affinity to SARS-CoV-2 viral proteins and the associated human proteins. We
also validate these predictions via auto-docking simulations and comparison
with recent experimental evidence, and step up the process of interpreting
machine learning prediction of protein-ligand binding by identifying potential
active binding sites on the amino acid sequence. Overall, AI-Bind offers a
powerful high-throughput approach to identify drug-target combinations, with
the potential of becoming a powerful tool in drug discovery.

21
The categories of this paper are: adap-org
23
The categories of this paper are: solv-int
27
The categories of this paper are: comp-gas
2
The categories of this paper are: math
6
The categories of this paper are: astro-ph
18
The categories of this paper are: econ
20
The categories of this paper are: acc-phys
30
The categories of this paper are: q-alg
19
The categories of this paper are: eess
9
The categories of this paper are: nlin
33
The categories of this paper are: plasm-ph
26
The categories of this paper are: bayes-an
31
The categories of this paper are: ao-sci
36
The categories of this paper are: cmp-lg
32
The categories of this paper are: atom-ph
7
The categories of this paper are: hep-th