Efficient prediction of anticancer peptides through deep learning.

Background: Cancer remains one of the leading causes of mortality globally, with conventional chemotherapy often resulting in severe side effects and limited effectiveness. Recent advancements in bioinformatics and machine learning, particularly deep learning, offer promising new avenues for cancer treatment through the prediction and identification of anticancer peptides. Objective: This study aimed to develop and evaluate a deep learning model utilizing a two-dimensional convolutional neural network (2D CNN) to enhance the prediction accuracy of anticancer peptides, addressing the complexities and limitations of current prediction methods. Methods: A diverse dataset of peptide sequences with annotated anticancer activity labels was compiled from various public databases and experimental studies. The sequences were preprocessed and encoded using one-hot encoding and additional physicochemical properties. The 2D CNN model was trained and optimized using this dataset, with performance evaluated through metrics such as accuracy, precision, recall, F1-score, and area under the receiver operating characteristic curve (AUC-ROC). Results: The proposed 2D CNN model achieved superior performance compared to existing methods, with an accuracy of 0.87, precision of 0.85, recall of 0.89, F1-score of 0.87, and an AUC-ROC value of 0.91. These results indicate the model's effectiveness in accurately predicting anticancer peptides and capturing intricate spatial patterns within peptide sequences. Conclusion: The findings demonstrate the potential of deep learning, specifically 2D CNNs, in advancing the prediction of anticancer peptides. The proposed model significantly improves prediction accuracy, offering a valuable tool for identifying effective peptide candidates for cancer treatment. Future Work: Further research should focus on expanding the dataset, exploring alternative deep learning architectures, and validating the model's predictions through experimental studies. Efforts should also aim at optimizing computational efficiency and translating these predictions into clinical applications.

ACP-GBDT: An improved anticancer peptide identification method with gradient boosting decision tree.

Cancer is one of the most dangerous diseases in the world, killing millions of people every year. Drugs composed of anticancer peptides have been used to treat cancer with low side effects in recent years. Therefore, identifying anticancer peptides has become a focus of research. In this study, an improved anticancer peptide predictor named ACP-GBDT, based on gradient boosting decision tree (GBDT) and sequence information, is proposed. To encode the peptide sequences included in the anticancer peptide dataset, ACP-GBDT uses a merged-feature composed of AAIndex and SVMProt-188D. A GBDT is adopted to train the prediction model in ACP-GBDT. Independent testing and ten-fold cross-validation show that ACP-GBDT can effectively distinguish anticancer peptides from non-anticancer ones. The comparison results of the benchmark dataset show that ACP-GBDT is simpler and more effective than other existing anticancer peptide prediction methods.

Drug-target binding affinity prediction method based on a deep graph neural network.

The development of new drugs is a long and costly process, Computer-aided drug design reduces development costs while computationally shortening the new drug development cycle, in which DTA (Drug-Target binding Affinity) prediction is a key step to screen out potential drugs. With the development of deep learning, various types of deep learning models have achieved notable performance in a wide range of fields. Most current related studies focus on extracting the sequence features of molecules while ignoring the valuable structural information; they employ sequence data that represent only the elemental composition of molecules without considering the molecular structure maps that contain structural information. In this paper, we use graph neural networks to predict DTA based on corresponding graph data of drugs and proteins, and we achieve competitive performance on two benchmark datasets, Davis and KIBA. In particular, an MSE of 0.227 and CI of 0.895 were obtained on Davis, and an MSE of 0.127 and CI of 0.903 were obtained on KIBA.

ISTRF: Identification of sucrose transporter using random forest.

Sucrose transporter (SUT) is a type of transmembrane protein that exists widely in plants and plays a significant role in the transportation of sucrose and the specific signal sensing process of sucrose. Therefore, identifying sucrose transporter is significant to the study of seed development and plant flowering and growth. In this study, a random forest-based model named ISTRF was proposed to identify sucrose transporter. First, a database containing 382 SUT proteins and 911 non-SUT proteins was constructed based on the UniProt and PFAM databases. Second, k-separated-bigrams-PSSM was exploited to represent protein sequence. Third, to overcome the influence of imbalance of samples on identification performance, the Borderline-SMOTE algorithm was used to overcome the shortcoming of imbalance training data. Finally, the random forest algorithm was used to train the identification model. It was proved by 10-fold cross-validation results that k-separated-bigrams-PSSM was the most distinguishable feature for identifying sucrose transporters. The Borderline-SMOTE algorithm can improve the performance of the identification model. Furthermore, random forest was superior to other classifiers on almost all indicators. Compared with other identification models, ISTRF has the best general performance and makes great improvements in identifying sucrose transporter proteins.

Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations.

Predicting protein properties from amino acid sequences is an important problem in biology and pharmacology. Protein-protein interactions among SARS-CoV-2 spike protein, human receptors and antibodies are key determinants of the potency of this virus and its ability to evade the human immune response. As a rapidly evolving virus, SARS-CoV-2 has already developed into many variants with considerable variation in virulence among these variants. Utilizing the proteomic data of SARS-CoV-2 to predict its viral characteristics will, therefore, greatly aid in disease control and prevention. In this paper, we review and compare recent successful prediction methods based on long short-term memory (LSTM), transformer, convolutional neural network (CNN) and a similarity-based topological regression (TR) model and offer recommendations about appropriate predictive methodology depending on the similarity between training and test datasets. We compare the effectiveness of these models in predicting the binding affinity and expression of SARS-CoV-2 spike protein sequences. We also explore how effective these predictive methods are when trained on laboratory-created data and are tasked with predicting the binding affinity of the in-the-wild SARS-CoV-2 spike protein sequences obtained from the GISAID datasets. We observe that TR is a better method when the sample size is small and test protein sequences are sufficiently similar to the training sequence. However, when the training sample size is sufficiently large and prediction requires extrapolation, LSTM embedding and CNN-based predictive model show superior performance.

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches.

With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine learning techniques are playing key roles in this field. Typically, predictors based on machine learning techniques contain three main steps: feature extraction, predictor construction and performance evaluation. Although several Web servers and stand-alone tools have been developed to facilitate the biological sequence analysis, they only focus on individual step. In this regard, in this study a powerful Web server called BioSeq-Analysis (http://bioinformatics.hitsz.edu.cn/BioSeq-Analysis/) has been proposed to automatically complete the three main steps for constructing a predictor. The user only needs to upload the benchmark data set. BioSeq-Analysis can generate the optimized predictor based on the benchmark data set, and the performance measures can be reported as well. Furthermore, to maximize user's convenience, its stand-alone program was also released, which can be downloaded from http://bioinformatics.hitsz.edu.cn/BioSeq-Analysis/download/, and can be directly run on Windows, Linux and UNIX. Applied to three sequence analysis tasks, experimental results showed that the predictors generated by BioSeq-Analysis even outperformed some state-of-the-art methods. It is anticipated that BioSeq-Analysis will become a useful tool for biological sequence analysis.

Extending hidden Markov models to allow conditioning on previous observations.

Hidden Markov Models (HMMs) are probabilistic models widely used in computational molecular biology. However, the Markovian assumption regarding transition probabilities which dictates that the observed symbol depends only on the current state may not be sufficient for some biological problems. In order to overcome the limitations of the first order HMM, a number of extensions have been proposed in the literature to incorporate past information in HMMs conditioning either on the hidden states, or on the observations, or both. Here, we implement a simple extension of the standard HMM in which the current observed symbol (amino acid residue) depends both on the current state and on a series of observed previous symbols. The major advantage of the method is the simplicity in the implementation, which is achieved by properly transforming the observation sequence, using an extended alphabet. Thus, it can utilize all the available algorithms for the training and decoding of HMMs. We investigated the use of several encoding schemes and performed tests in a number of important biological problems previously studied by our team (prediction of transmembrane proteins and prediction of signal peptides). The evaluation shows that, when enough data are available, the performance increased by 1.8%-8.2% and the existing prediction methods may improve using this approach. The methods, for which the improvement was significant (PRED-TMBB2, PRED-TAT and HMM-TM), are available as web-servers freely accessible to academic users at www.compgen.org/tools/ .