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

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.

IFoodCloud: A Platform for Real-time Sentiment Analysis of Public Opinion about Food Safety in China

The Internet contains a wealth of public opinion on food safety, including views on food adulteration, food-borne diseases, agricultural pollution, irregular food distribution, and food production issues. In order to systematically collect and analyse public opinion on food safety, we developed IFoodCloud, a platform for the real-time sentiment analysis of public opinion on food safety in China. It collects data from more than 3,100 public sources that can be used to explore public opinion trends, public sentiment, and regional attention differences of food safety incidents. At the same time, we constructed a sentiment classification model using multiple lexicon-based and deep learning-based algorithms integrated with IFoodCloud that provide an unprecedented rapid means of understanding the public sentiment toward specific food safety incidents. Our best model's F1-score achieved 0.9737. Further, three real-world cases are presented to demonstrate the application and robustness. IFoodCloud could be considered a valuable tool for promote scientisation of food safety supervision and risk communication.