Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any pre-computed physics-inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end-to-end learning from molecular structures containing tens of thousands of atoms: a point-based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

In symbolic regression, the search for analytic models is typically driven purely by the prediction error observed on the training data samples. However, when the data samples do not sufficiently cover the input space, the prediction error does not provide sufficient guidance toward desired models. Standard symbolic regression techniques then yield models that are partially incorrect, for instance, in terms of their steady-state characteristics or local behavior. If these properties were considered already during the search process, more accurate and relevant models could be produced. We propose a multi-objective symbolic regression approach that is driven by both the training data and the prior knowledge of the properties the desired model should manifest. The properties given in the form of formal constraints are internally represented by a set of discrete data samples on which candidate models are exactly checked. The proposed approach was experimentally evaluated on three test problems with results clearly demonstrating its capability to evolve realistic models that fit the training data well while complying with the prior knowledge of the desired model characteristics at the same time. It outperforms standard symbolic regression by several orders of magnitude in terms of the mean squared deviation from a reference model.