Academy & Industry Research Collaboration Center (AIRCC)

Volume 10, Number 02, March 2020

Meramalnet: A Deep Learning Convolutional Neural Network for Bioactivity Prediction
in Structure-based Drug Discovery


Hentabli Hamza1, Naomie Salim1, Maged Nasser1 and Faisal Saeed2, 1Universiti Teknologi Malaysia, Malaysia and 2Taibah University, Saudi Arabia


According to the principle of similar property, structurally similar compounds exhibit very similar properties and, also, similar biological activities. Many researchers have applied this principle to discovering novel drugs, which has led to the emergence of the chemical structure-based activity prediction. Using this technology, it becomes easier to predict the activities of unknown compounds (target) by comparing the unknown target compounds with a group of already known chemical compounds. Thereafter, the researcher assigns the activities of the similar and known compounds to the target compounds. Various Machine Learning (ML) techniques have been used for predicting the activity of the compounds. In this study, the researchers have introduced a novel predictive system, i.e., MaramalNet, which is a convolutional neural network that enables the prediction of molecular bioactivities using a different molecular matrix representation. MaramalNet is a deep learning system which also incorporates the substructure information with regards to the molecule for predicting its activity. The researchers have investigated this novel convolutional network for determining its accuracy during the prediction of the activities for the unknown compounds. This approach was applied to a popular dataset and the performance of this system was compared with three other classical ML algorithms. All experiments indicated that MaramalNet was able to provide an interesting prediction rate (where the highly diverse dataset showed 88.01% accuracy, while a low diversity dataset showed 99% accuracy). Also, MaramalNet was seen to be very effective for the homogeneous datasets but showed a lower performance in the case of the structurally heterogeneous datasets.


Bioactive Molecules, Activity prediction model, Convolutional neural network, Deep Learning, biological activities