Soil organic matter (SOM) is an important source of nutrients required during crop growth and is an important component of cultivated soil. In this paper, we studied the possibility of using deep learning methods to establish a multi-feature model to predict SOM content. Moreover, using Nong’an County of Changchun City as the study area, Sentinel-2A remote sensing images were taken as the data source to construct the dataset by using field sampling and image processing. The LeNet-5 convolutional neural network model was chosen as the deep learning model, which was improved based on the basic model. The evaluation metrics were selected as the root mean square error (RMSE) and the coefficient of determination R². Through comparison, the R² of the improved model was found to be higher than that of the linear regression method, Support Vector Machines (SVM) (RMSE = 2.471, R² = 0.4035), and Random Forest (RF) (RMSE = 2.577, R² = 0.4913). The result shows that: (1) It is feasible to use the multispectral data extracted from remote sensing images for soil organic matter content inversion based on the deep learning model with a minimum RMSE of 2.979 and with the R² reaching 0.89. (2) The choice of features has an impact on the prediction of the model to a certain extent. After ranking the importance of features, selecting the appropriate number of features for inversion provides better results than full feature inversion, and the computational speed is improved.

Background: Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. However, existing methods generally rely on feature engineering, and ignore the natural similarity between the two types of protein translational modification. This study is the first all-in-one deep network to predict protein Ubiquitylation and SUMOylation sites from protein sequences as well as their crosstalk sites simultaneously. Our deep learning architecture integrates several meta classifiers that apply deep neural networks to protein sequence information and physico-chemical properties, which were trained on multi-label classification mode for simultaneously identifying protein Ubiquitylation and SUMOylation as well as their crosstalk sites. Results: The promising AUCs of our method on Ubiquitylation, SUMOylation and crosstalk sites achieved 0.838, 0.888, and 0.862 respectively on tenfold cross-validation. The corresponding APs reached 0.683, 0.804 and 0.552, which also validated our effectiveness. Conclusions: The proposed architecture managed to classify ubiquitylated and SUMOylated lysine residues along with their crosstalk sites, and outperformed other well-known Ubiquitylation and SUMOylation site prediction tools.

Protein-protein docking reveals the process and product in protein interactions. Typically, a protein docking works with a docking model sampling, and then an evaluation method is used to rank the near-native models out from a large pool of generated decoys. In practice, the evaluation stage is the bottleneck to perform accurate protein docking. In this paper, PointNet, a deep learning algorithm based on point cloud, is applied to evaluate protein docking models. The proposed architecture is able to directly learn deep representations carrying the geometrical properties and atomic attributes from the 3D structural data of protein decoys. The experimental results show that the informative representations can benefit our proposed method to outperform other algorithms.

N-terminal acetylation is a specific protein modification that occurs only at the N-terminus but plays a significant role in protein stability, folding, subcellular localization and protein-protein interactions. Computational methods enable finding N-terminal acetylated sites from large-scale proteins efficiently. However, limited by the number of the labeled proteins, existing tools only focus on certain subtypes of N-terminal acetylated sites on frequently detected amino acids. For example, NetAcet focuses on alanine, glycine, serine and threonine only, and N-Ace predicts on alanine, glycine, methionine, serine and threonine. With the growth of experimental N-terminal acetylated site data, it is observed that N-terminal protein acetylation occurs on nearly ten types of amino acids. To facilitate comprehensive analysis, we have developed MTNA (Multiple Types of N-terminal Acetylation), a deep learning network capable of accurately predicting N-terminal protein acetylation sites for various amino acids at the N-terminus. MTNA not only outperforms existing tools but also has the capability to identify rare types of N-terminal protein acetylated sites occurring on less studied amino acids.