Deep Learning-Based Potential Ligand Prediction Framework for COVID-19 with Drug-Target Interaction Model.
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ABSTRACT:
SUBMITTER: Majumdar S
PROVIDER: S-EPMC7852055 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:SummaryAccurate prediction of drug-target interactions (DTI) is crucial for drug discovery. Recently, deep learning (DL) models for show promising performance for DTI prediction. However, these models can be difficult to use for both computer scientists entering the biomedical field and bioinformaticians with limited DL experience. We present DeepPurpose, a comprehensive and easy-to-use DL library for DTI prediction. DeepPurpose supports training of customized DTI prediction models by implementing 15 compound and protein encoders and over 50 neural architectures, along with providing many other useful features. We demonstrate state-of-the-art performance of DeepPurpose on several benchmark datasets.Availability and implementationhttps://github.com/kexinhuang12345/DeepPurpose.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8016467 | biostudies-literature
Project description:BACKGROUND:Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target proteins. In recent studies, handcrafted features, similarity metrics and machine learning methods have been proposed for predicting drug-target interactions. However, these methods cannot fully learn the underlying relations between drugs and targets. In this paper, we propose anew framework for drug-target interaction prediction that learns latent features from drug-target interaction network. RESULTS:We present a framework to utilize the network topology and identify interacting and non-interacting drug-target pairs. We model the problem as a semi-bipartite graph in which we are able to use drug-drug and protein-protein similarity in a drug-protein network. We have then used a graph labeling method for vertex ordering in our graph embedding process. Finally, we employed deep neural network to learn the complex pattern of interacting pairs from embedded graphs. We show our approach is able to learn sophisticated drug-target topological features and outperforms other state-of-the-art approaches. CONCLUSIONS:The proposed learning model on semi-bipartite graph model, can integrate drug-drug and protein-protein similarities which are semantically different than drug-protein information in a drug-target interaction network. We show our model can determine interaction likelihood for each drug-target pair and outperform other heuristics.
| S-EPMC7336396 | biostudies-literature
Project description:Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the modern drug discovery pipeline as it mitigates the cost, time, and resources required to screen novel therapeutics. Deep Neural Networks (DNN) have recently shown excellent performance in PLI prediction. However, the performance is highly dependent on protein and ligand features utilized for the DNN model. Moreover, in current models, the deciphering of how protein features determine the underlying principles that govern PLI is not trivial. In this work, we developed a DNN framework named SSnet that utilizes secondary structure information of proteins extracted as the curvature and torsion of the protein backbone to predict PLI. We demonstrate the performance of SSnet by comparing against a variety of currently popular machine and non-Machine Learning (ML) models using various metrics. We visualize the intermediate layers of SSnet to show a potential latent space for proteins, in particular to extract structural elements in a protein that the model finds influential for ligand binding, which is one of the key features of SSnet. We observed in our study that SSnet learns information about locations in a protein where a ligand can bind, including binding sites, allosteric sites and cryptic sites, regardless of the conformation used. We further observed that SSnet is not biased to any specific molecular interaction and extracts the protein fold information critical for PLI prediction. Our work forms an important gateway to the general exploration of secondary structure-based Deep Learning (DL), which is not just confined to protein-ligand interactions, and as such will have a large impact on protein research, while being readily accessible for de novo drug designers as a standalone package.
| S-EPMC7869013 | biostudies-literature
Project description:Peptide-protein interactions are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. Recently, a number of computational methods have been developed to predict peptide-protein interactions. However, most of the existing prediction approaches heavily depend on high-resolution structure data. Here, we present a deep learning framework for multi-level peptide-protein interaction prediction, called CAMP, including binary peptide-protein interaction prediction and corresponding peptide binding residue identification. Comprehensive evaluation demonstrated that CAMP can successfully capture the binary interactions between peptides and proteins and identify the binding residues along the peptides involved in the interactions. In addition, CAMP outperformed other state-of-the-art methods on binary peptide-protein interaction prediction. CAMP can serve as a useful tool in peptide-protein interaction prediction and identification of important binding residues in the peptides, which can thus facilitate the peptide drug discovery process.
| S-EPMC8443569 | biostudies-literature
Project description: Not available
| S-EPMC10998640 | biostudies-literature
Project description:BackgroundPredicting the effect of drug-drug interactions (DDIs) precisely is important for safer and more effective drug co-prescription. Many computational approaches to predict the effect of DDIs have been proposed, with the aim of reducing the effort of identifying these interactions in vivo or in vitro, but room remains for improvement in prediction performance.ResultsIn this study, we propose a novel deep learning model to predict the effect of DDIs more accurately.. The proposed model uses autoencoders and a deep feed-forward network that are trained using the structural similarity profiles (SSP), Gene Ontology (GO) term similarity profiles (GSP), and target gene similarity profiles (TSP) of known drug pairs to predict the pharmacological effects of DDIs. The results show that GSP and TSP increase the prediction accuracy when using SSP alone, and the autoencoder is more effective than PCA for reducing the dimensions of each profile. Our model showed better performance than the existing methods, and identified a number of novel DDIs that are supported by medical databases or existing research.ConclusionsWe present a novel deep learning model for more accurate prediction of DDIs and their effects, which may assist in future research to discover novel DDIs and their pharmacological effects.
| S-EPMC6685287 | biostudies-literature
Project description:BACKGROUND:The key to modern drug discovery is to find, identify and prepare drug molecular targets. However, due to the influence of throughput, precision and cost, traditional experimental methods are difficult to be widely used to infer these potential Drug-Target Interactions (DTIs). Therefore, it is urgent to develop effective computational methods to validate the interaction between drugs and target. METHODS:We developed a deep learning-based model for DTIs prediction. The proteins evolutionary features are extracted via Position Specific Scoring Matrix (PSSM) and Legendre Moment (LM) and associated with drugs molecular substructure fingerprints to form feature vectors of drug-target pairs. Then we utilized the Sparse Principal Component Analysis (SPCA) to compress the features of drugs and proteins into a uniform vector space. Lastly, the deep long short-term memory (DeepLSTM) was constructed for carrying out prediction. RESULTS:A significant improvement in DTIs prediction performance can be observed on experimental results, with AUC of 0.9951, 0.9705, 0.9951, 0.9206, respectively, on four classes important drug-target datasets. Further experiments preliminary proves that the proposed characterization scheme has great advantage on feature expression and recognition. We also have shown that the proposed method can work well with small dataset. CONCLUSION:The results demonstration that the proposed approach has a great advantage over state-of-the-art drug-target predictor. To the best of our knowledge, this study first tests the potential of deep learning method with memory and Turing completeness in DTIs prediction.
| S-EPMC7079345 | biostudies-literature
Project description:Drug-target interaction (DTI) prediction is a crucial step in drug discovery and repositioning as it reduces experimental validation costs if done right. Thus, developing in-silico methods to predict potential DTI has become a competitive research niche, with one of its main focuses being improving the prediction accuracy. Using machine learning (ML) models for this task, specifically network-based approaches, is effective and has shown great advantages over the other computational methods. However, ML model development involves upstream hand-crafted feature extraction and other processes that impact prediction accuracy. Thus, network-based representation learning techniques that provide automated feature extraction combined with traditional ML classifiers dealing with downstream link prediction tasks may be better-suited paradigms. Here, we present such a method, DTi2Vec, which identifies DTIs using network representation learning and ensemble learning techniques. DTi2Vec constructs the heterogeneous network, and then it automatically generates features for each drug and target using the nodes embedding technique. DTi2Vec demonstrated its ability in drug-target link prediction compared to several state-of-the-art network-based methods, using four benchmark datasets and large-scale data compiled from DrugBank. DTi2Vec showed a statistically significant increase in the prediction performances in terms of AUPR. We verified the "novel" predicted DTIs using several databases and scientific literature. DTi2Vec is a simple yet effective method that provides high DTI prediction performance while being scalable and efficient in computation, translating into a powerful drug repositioning tool.
| S-EPMC8459562 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-03-31 | GSE165175 | GEO
Project description:Artificial intelligence (AI) is undergoing a revolution thanks to the breakthroughs of machine learning algorithms in computer vision, speech recognition, natural language processing and generative modelling. Recent works on publicly available pharmaceutical data showed that AI methods are highly promising for Drug Target prediction. However, the quality of public data might be different than that of industry data due to different labs reporting measurements, different measurement techniques, fewer samples and less diverse and specialized assays. As part of a European funded project (ExCAPE), that brought together expertise from pharmaceutical industry, machine learning, and high-performance computing, we investigated how well machine learning models obtained from public data can be transferred to internal pharmaceutical industry data. Our results show that machine learning models trained on public data can indeed maintain their predictive power to a large degree when applied to industry data. Moreover, we observed that deep learning derived machine learning models outperformed comparable models, which were trained by other machine learning algorithms, when applied to internal pharmaceutical company datasets. To our knowledge, this is the first large-scale study evaluating the potential of machine learning and especially deep learning directly at the level of industry-scale settings and moreover investigating the transferability of publicly learned target prediction models towards industrial bioactivity prediction pipelines.
| S-EPMC7169028 | biostudies-literature