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

TL;DR

EMOCPD introduces an attention-based deep learning model that predicts amino acid categories from protein microenvironments, significantly improving accuracy and aiding in the design of more stable, expressive proteins.

Contribution

This paper presents EMOCPD, a novel attention-based neural network that effectively analyzes sparse protein microenvironments for improved computational protein design.

Findings

Achieves over 80% accuracy on training data

Surpasses existing methods by over 10% on test sets

Enhances protein stability and expression in designed mutants

Abstract

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.