Thermophilic proteins have great potential to be utilized as biocatalysts in biotechnology. Machine learning algorithms are gaining increasing use in identifying such enzymes, reducing or even eliminating the need for experimental studies. While most previously used machine learning methods were based on manually designed features, we developed BertThermo, a model using Bidirectional Encoder Representations from Transformers (BERT), as an automatic feature extraction tool. This method combines a variety of machine learning algorithms and feature engineering methods, while relying on single-feature encoding based on the protein sequence alone for model input. BertThermo achieved an accuracy of 96.97% and 97.51% in 5-fold cross-validation and in independent testing, respectively, identifying thermophilic proteins more reliably than any previously described predictive algorithm. Additionally, BertThermo was tested by a balanced dataset, an imbalanced dataset and a dataset with homology sequences, and the results show that BertThermo was with the best robustness as comparied with state-of-the-art methods. The source code of BertThermo is available.

Umami peptides enhance the umami taste of food and have good food processing properties, nutritional value, and numerous potential applications. Wet testing for the identification of umami peptides is a time-consuming and expensive process. Here, we report the iUmami-DRLF that uses a logistic regression (LR) method solely based on the deep learning pre-trained neural network feature extraction method, unified representation (UniRep based on multiplicative LSTM), for feature extraction from the peptide sequences. The findings demonstrate that deep learning representation learning significantly enhanced the capability of models in identifying umami peptides and predictive precision solely based on peptide sequence information. The newly validated taste sequences were also used to test the iUmami-DRLF and other predictors, and the result indicates that the iUmami-DRLF has better robustness and accuracy and remains valid at higher probability thresholds. The iUmami-DRLF method can aid further studies on enhancing the umami flavor of food for satisfying the need for an umami-flavored diet.

Anti-coronavirus peptides (ACVPs) represent a relatively novel approach of inhibiting the adsorption and fusion of the virus with human cells. Several peptide-based inhibitors showed promise as potential therapeutic drug candidates. However, identifying such peptides in laboratory experiments is both costly and time consuming. Therefore, there is growing interest in using computational methods to predict ACVPs. Here, we describe a model for the prediction of ACVPs that is based on the combination of feature engineering (FE) optimization and deep representation learning. FEOpti-ACVP was pre-trained using two feature extraction frameworks. At the next step, several machine learning approaches were tested in to construct the final algorithm. The final version of FEOpti-ACVP outperformed existing methods used for ACVPs prediction and it has the potential to become a valuable tool in ACVP drug design. A user-friendly webserver of FEOpti-ACVP can be accessed at http://servers.aibiochem.net/soft/FEOpti-ACVP/.

Anticancer peptides (ACPs) represent a promising new therapeutic approach in cancer treatment. They can target cancer cells without affecting healthy tissues or altering normal physiological functions. Machine learning algorithms have increasingly been utilized for predicting peptide sequences with potential ACP effects. This study analyzed four benchmark datasets based on a well-established random forest (RF) algorithm. The peptide sequences were converted into 566 physicochemical features extracted from the amino acid index (AAindex) library, which were then subjected to feature selection using four methods: light gradient-boosting machine (LGBM), analysis of variance (ANOVA), chi-squared test (Chi²), and mutual information (MI). Presenting and merging the identified features using Venn diagrams, 19 key amino acid physicochemical properties were identified that can be used to predict the likelihood of a peptide sequence functioning as an ACP. The results were quantified by performance evaluation metrics to determine the accuracy of predictions. This study aims to enhance the efficiency of designing peptide sequences for cancer treatment.

Interleukin-10 (IL-10) has anti-inflammatory properties and is a crucial cytokine in regulating immunity. The identification of IL-10 through wet laboratory experiments is costly and time-intensive. Therefore, a new IL-10-induced peptide recognition method, IL10-Stack, was introduced in this research, which was based on unified deep representation learning and a stacking algorithm. Two approaches were employed to extract features from peptide sequences: Amino Acid Index (AAindex) and sequence-based unified representation (UniRep). After feature fusion and optimized feature selection, we selected a 1900-dimensional UniRep feature vector and constructed the IL10-Stack model using stacking. IL10-Stack exhibited excellent performance in IL-10-induced peptide recognition (accuracy (ACC) = 0.910, Matthews correlation coefficient (MCC) = 0.820). Relative to the existing methods, IL-10Pred and ILeukin10Pred, the approach increased in ACC by 12.1% and 2.4%, respectively. The IL10-Stack method can identify IL-10-induced peptides, which aids in the development of immunosuppressive drugs.