# ResAtom System: Protein and Ligand Affinity Prediction Model Based on Deep Learning

arXiv: https://arxiv.org/abs/2105.05125 · HTML: https://mlsanity.com/paper/2105.05125/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 6 of its 47 references that are in the map.
- First posted on arXiv 17 Apr 2021.

## Builds on (most cited first, 6 of 6)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [An Introduction to Convolutional Neural Networks](https://mlsanity.com/paper/1511.08458/) (2015)
- [TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning](https://mlsanity.com/paper/2003.04696/) (2020)
- [Protein-Ligand Scoring with Convolutional Neural Networks](https://mlsanity.com/paper/1612.02751/) (2016)

## Built on by (most cited first, 1 of 1)

- [Target-Free Compound Activity Prediction via Few-Shot Learning](https://mlsanity.com/paper/2311.16328/) (2023)

## Abstract (arXiv)

Motivation: Protein-ligand affinity prediction is an important part of structure-based drug design. It includes molecular docking and affinity prediction. Although molecular dynamics can predict affinity with high accuracy at present, it is not suitable for large-scale virtual screening. The existing affinity prediction and evaluation functions based on deep learning mostly rely on experimentally-determined conformations. Results: We build a predictive model of protein-ligand affinity through the ResNet neural network with added attention mechanism. The resulting ResAtom-Score model achieves Pearson's correlation coefficient R = 0.833 on the CASF-2016 benchmark test set. At the same time, we evaluated the performance of a variety of existing scoring functions in combination with ResAtom-Score in the absence of experimentally-determined conformations. The results show that the use of DeltaVinaRF20 in combination with ResAtom-Score can achieve affinity prediction close to scoring functions in the presence of experimentally-determined conformations. These results suggest that ResAtom system may be used for in silico screening of small molecule ligands with target proteins in the future. Availability: https://github.com/wyji001/ResAtom