Convolutional neural network with stacked autoencoders for predicting drug-target interaction and binding affinity

2021 ◽  
Vol 13 (1/2) ◽  
pp. 81
Author(s):  
Meriem Bahi ◽  
Mohamed Batouche
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Binding Affinity ◽  
Drug Target ◽  
Target Interaction ◽  
Stacked Autoencoders

scholarly journals FRnet-DTI: Deep convolutional neural network for drug-target interaction prediction

Heliyon ◽  
2020 ◽  
Vol 6 (3) ◽  
pp. e03444 ◽  
Author(s):  
Farshid Rayhan ◽  
Sajid Ahmed ◽  
Zaynab Mousavian ◽  
Dewan Md Farid ◽  
Swakkhar Shatabda
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Drug Target ◽  
Deep Convolutional Neural Network ◽  
Target Interaction ◽  
Interaction Prediction

scholarly journals Prediction of drug–target binding affinity using similarity-based convolutional neural network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jooyong Shim ◽  
Zhen-Yu Hong ◽  
Insuk Sohn ◽  
Changha Hwang
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Binding Affinity ◽  
Drug Target ◽  
Binary Classification ◽  
Binding Affinities ◽  
Binding Affinity Prediction ◽  
Affinity Prediction ◽  
Target Binding ◽  
Public Datasets

AbstractIdentifying novel drug–target interactions (DTIs) plays an important role in drug discovery. Most of the computational methods developed for predicting DTIs use binary classification, whose goal is to determine whether or not a drug–target (DT) pair interacts. However, it is more meaningful but also more challenging to predict the binding affinity that describes the strength of the interaction between a DT pair. If the binding affinity is not sufficiently large, such drug may not be useful. Therefore, the methods for predicting DT binding affinities are very valuable. The increase in novel public affinity data available in the DT-related databases enables advanced deep learning techniques to be used to predict binding affinities. In this paper, we propose a similarity-based model that applies 2-dimensional (2D) convolutional neural network (CNN) to the outer products between column vectors of two similarity matrices for the drugs and targets to predict DT binding affinities. To our best knowledge, this is the first application of 2D CNN in similarity-based DT binding affinity prediction. The validation results on multiple public datasets show that the proposed model is an effective approach for DT binding affinity prediction and can be quite helpful in drug development process.

scholarly journals OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells

2021 ◽  
Vol 9 ◽  
Author(s):  
Zechen Wang ◽  
Liangzhen Zheng ◽  
Yang Liu ◽  
Yuanyuan Qu ◽  
Yong-Qiang Li ◽  
...  
Keyword(s):  
Neural Network ◽  
Ligand Binding ◽  
Convolutional Neural Network ◽  
Binding Affinity ◽  
Binding Free Energy ◽  
Computational Cost ◽  
Scoring Function ◽  
Quality Data ◽  
Great Success ◽  
Data Set

One key task in virtual screening is to accurately predict the binding affinity (△G) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the extraordinary ability of DL to extract useful features from raw data. Nevertheless, more efforts still need to be paid in many aspects, for the aim of increasing prediction accuracy and decreasing computational cost. In this study, we proposed a simple scoring function (called OnionNet-2) based on convolutional neural network to predict △G. The protein-ligand interactions are characterized by the number of contacts between protein residues and ligand atoms in multiple distance shells. Compared to published models, the efficacy of OnionNet-2 is demonstrated to be the best for two widely used datasets CASF-2016 and CASF-2013 benchmarks. The OnionNet-2 model was further verified by non-experimental decoy structures from docking program and the CSAR NRC-HiQ data set (a high-quality data set provided by CSAR), which showed great success. Thus, our study provides a simple but efficient scoring function for predicting protein-ligand binding free energy.

scholarly journals RosENet: Improving binding affinity prediction by leveraging molecular mechanics energies with a 3D Convolutional Neural Network

2020 ◽  
Author(s):  
Hussein Hassan-Harrirou ◽  
Ce Zhang ◽  
Thomas Lemmin
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Molecular Mechanics ◽  
Binding Affinity ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Search Space ◽  
Screening Experiments ◽  
Physico Chemical ◽  
Dynamics Simulations

ABSTRACTThe worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key step in these approaches is the need for the rapid and accurate prediction of the binding affinity for potential leads.Here, we present RosENet (Rosetta Energy Neural Network), a three-dimensional (3D) Convolutional Neural Network (CNN), which combines voxelized molecular mechanics energies and molecular descriptors for predicting the absolute binding affinity of protein – ligand complexes. By leveraging the physico-chemical properties captured by the molecular force field, our model achieved a Root Mean Square Error (RMSE) of 1.26 on the PDBBind v2016 core set. We also explored some limitations and the robustness of the PDBBind dataset and our approach, on nearly 500 structures, including structures determined by Nuclear Magnetic Resonance and virtual screening experiments. Our study demonstrated that molecular mechanics energies can be voxelized and used to help improve the predictive power of the CNNs. In the future, our framework can be extended to features extracted from other biophysical and biochemical models, such as molecular dynamics simulations.Availabilityhttps://github.com/DS3Lab/RosENet

Predicting drug-target affinity based on recurrent neural networks and graph convolutional neural networks

2021 ◽  
Vol 24 ◽  
Author(s):  
Qingyu Tian ◽  
Mao Ding ◽  
Hui Yang ◽  
Caibin Yue ◽  
Yue Zhong ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Time Series ◽  
Convolutional Neural Network ◽  
Drug Target ◽  
Channel Model ◽  
Search Space ◽  
Topological Features ◽  
Latent Features ◽  
Chemical Background

Background: Drug development requires a lot of money and time, and the outcome of the challenge is unknown. So, there is an urgent need for researchers to find a new approach that can reduce costs. Therefore, the identification of drug-target interactions (DTIs) has been a critical step in the early stages of drug discovery. These computational methods aim to narrow the search space for novel DTIs and to elucidate the functional background of drugs. Most of the methods developed so far use binary classification to predict the presence or absence of interactions between the drug and the target. However, it is more informative, but also more challenging, to predict the strength of the binding between a drug and its target. If the strength is not strong enough, such a DTI may not be useful. Hence, the development of methods to predict drug-target affinity (DTA) is of significant importance. Method: We have improved the Graph DTA model from a dual-channel model to a triple-channel model. We interpreted the target/protein sequences as time series and extracted their features using the LSTM network. For the drug, we considered both the molecular structure and the local chemical background, retaining the four variant networks used in Graph DTA to extract the topological features of the drug and capturing the local chemical background of the atoms in the drug by using BiGRU. Thus, we obtained the latent features of the target and two latent features of the drug. The connection of these three feature vectors is then input into a 2-layer FC network, and a valuable binding affinity is output. Result: We use the Davis and Kiba datasets, using 80% of the data for training and 20% of the data for validation. Our model shows better performance by comparing it with the experimental results of Graph DTA. Conclusion: In this paper, we altered the Graph DTA model to predict drug-target affinity. It represents the drug as a graph, and extracts the two-dimensional drug information using a graph convolutional neural network. Simultaneously, the drug and protein targets are represented as a word vector, and the convolutional neural network is used to extract the time series information of the drug and the target. We demonstrate that our improved method has better performance than the original method. In particular, our model has better performance in the evaluation of benchmark databases.

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