# EMOCPD: Efficient Attention-based Models for Computational Protein Design Using Amino Acid Microenvironment

arXiv: https://arxiv.org/abs/2410.21069 · HTML: https://mlsanity.com/paper/2410.21069/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 49 references that are in the map.
- First posted on arXiv 28 Oct 2024.

## Builds on (most cited first, 12 of 12)

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- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [Do Androids Laugh at Electric Sheep? Humor "Understanding" Benchmarks from The New Yorker Caption Contest](https://mlsanity.com/paper/2209.06293/) (2022)
- [Deep Learning for Computational Chemistry](https://mlsanity.com/paper/1701.04503/) (2017)

## Abstract (arXiv)

Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data era in biomolecules, with their accuracy limited by the energy functions and search algorithms. Existing deep learning methods are constrained by the learning capabilities of the networks, failing to extract effective information from sparse protein structures, which limits the accuracy of protein design. To address these shortcomings, we developed an Efficient attention-based Models for Computational Protein Design using amino acid microenvironment (EMOCPD). It aims to predict the category of each amino acid in a protein by analyzing the three-dimensional atomic environment surrounding the amino acids, and optimize the protein based on the predicted high-probability potential amino acid categories. EMOCPD employs a multi-head attention mechanism to focus on important features in the sparse protein microenvironment and utilizes an inverse residual structure to optimize the network architecture. The proposed EMOCPD achieves over 80% accuracy on the training set and 68.33% and 62.32% accuracy on two independent test sets, respectively, surpassing the best comparative methods by over 10%. In protein design, the thermal stability and protein expression of the predicted mutants from EMOCPD show significant improvements compared to the wild type, effectively validating EMOCPD's potential in designing superior proteins. Furthermore, the predictions of EMOCPD are influenced positively, negatively, or have minimal impact based on the content of the 20 amino acids, categorizing amino acids as positive, negative, or neutral. Research findings indicate that EMOCPD is more suitable for designing proteins with lower contents of negative amino acids.