  Accurate prediction of protein-ligand binding affinity is crucial for rapid
and efficient drug development. Recently, the importance of predicting binding
affinity has led to increased attention on research that models the
three-dimensional structure of protein-ligand complexes using graph neural
networks to predict binding affinity. However, traditional methods often fail
to accurately model the complex's spatial information or rely solely on
geometric features, neglecting the principles of protein-ligand binding. This
can lead to overfitting, resulting in models that perform poorly on independent
datasets and ultimately reducing their usefulness in real drug development. To
address this issue, we propose SPIN, a model designed to achieve superior
generalization by incorporating various inductive biases applicable to this
task, beyond merely training on empirical data from datasets. For prediction,
we defined two types of inductive biases: a geometric perspective that
maintains consistent binding affinity predictions regardless of the complexs
rotations and translations, and a physicochemical perspective that necessitates
minimal binding free energy along their reaction coordinate for effective
protein-ligand binding. These prior knowledge inputs enable the SPIN to
outperform comparative models in benchmark sets such as CASF-2016 and CSAR HiQ.
Furthermore, we demonstrated the practicality of our model through virtual
screening experiments and validated the reliability and potential of our
proposed model based on experiments assessing its interpretability.
