Hybrid-Enhanced Siamese Similarity Models in Ligand-Based Virtual Screen

Abstract

Information technology has become an integral aspect of the drug development process. The virtual screening process (VS) is a computational technique for screening chemical compounds in a reasonable amount of time and cost. The similarity search is one of the primary tasks in VS that estimates a molecule’s similarity. It is predicated on the idea that molecules with similar structures may also have similar activities. Many techniques for comparing the biological similarity between a target compound and each compound in the database have been established. Although the approaches have a strong performance, particularly when dealing with molecules with homogenous active structural, they are not enough good when dealing with structurally heterogeneous compounds. The previous works examined many deep learning methods in the enhanced Siamese similarity model and demonstrated that the Enhanced Siamese Multi-Layer Perceptron similarity model (SMLP) and the Siamese Convolutional Neural Network-one dimension similarity model (SCNN1D) have good outcomes when dealing with structurally heterogeneous molecules. To further improve the retrieval effectiveness of the similarity model, we incorporate the best two models in one hybrid model. The reason is that each method gives good results in some classes, so combining them in one hybrid model may improve the retrieval recall. Many designs of the hybrid models will be tested in this study. Several experiments on real-world data sets were conducted, and the findings demonstrated that the new approaches outperformed the previous method.

Deep Learning Based Methods for Molecular Similarity Searching: A Systematic Review

“…The effect of different weighting schemes on the utility of molecular similarity measures has been the subject of interesting studies [7,127]. In addition to the further extended literature related to the structure descriptors [81,128] and the similarity coefficients [1,3,24], several research articles have employed weighting schemes to improve the recall and accuracy performances [7,8,77,127,129,130]. It is based on this concept that non-related molecular fragments weigh equally to the relevant fragments in terms of biological activity.…”