Related papers: Advancing Ligand-based Virtual Screening and Molec…

Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…

Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…

Search behaviour is characterised using synonymy and polysemy as users often want to search information based on meaning. Semantic representation strategies represent a move towards richer associative connections that can adequately capture…

Virtual screening aims to efficiently identify active ligands from massive chemical libraries for a given target pocket. Recent CLIP-style models such as DrugCLIP enable scalable virtual screening by embedding pockets and ligands into a…

The three-dimensional shape and conformation of small-molecule ligands are critical for biomolecular recognition, yet encoding 3D geometry has not improved ligand-based virtual screening approaches. We describe an end-to-end deep learning…

The Graph Edit Distance (GED) is an important metric for measuring the similarity between two (labeled) graphs. It is defined as the minimum cost required to convert one graph into another through a series of (elementary) edit operations.…

We propose a novel molecular fingerprint-based variational autoencoder applied for molecular generation on real-world drug molecules. We define more suitable and pharma-relevant baseline metrics and tests, focusing on the generation of…

Low-dimensional embeddings are widely used as visual summaries of high-dimensional data and to enable downstream scientific discoveries. Yet, popular nonlinear dimension reduction methods, such as t-SNE and UMAP, are often selected based on…

Structure-based drug design aims at generating high affinity ligands with prior knowledge of 3D target structures. Existing methods either use conditional generative model to learn the distribution of 3D ligands given target binding sites,…

The growing demand for molecules with tailored properties in fields such as drug discovery and chemical engineering has driven advancements in computational methods for molecular design. Machine learning-based approaches for de-novo…

Similarity searching of molecular structure has been an important application in the Chemoinformatics, especially in drug discovery. Similarity searching is a common method used for identification of molecular structure. It involve three…

Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to…

The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without…

It is well-understood that different algorithms, training processes, and corpora produce different word embeddings. However, less is known about the relation between different embedding spaces, i.e. how far different sets of embeddings…

The precise diagnosis of urinary stones is crucial for devising effective treatment strategies. The diagnostic process, however, is often complicated by the low contrast between stones and surrounding tissues, as well as the variability in…

Edit-distance-based string similarity search has many applications such as spell correction, data de-duplication, and sequence alignment. However, computing edit distance is known to have high complexity, which makes string similarity…

Molecular property prediction is essential for drug discovery. In recent years, deep learning methods have been introduced to this area and achieved state-of-the-art performances. However, most of existing methods ignore the intrinsic…

Structure-based drug design, i.e., finding molecules with high affinities to the target protein pocket, is one of the most critical tasks in drug discovery. Traditional solutions, like virtual screening, require exhaustively searching on a…

Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…

The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i.e., a ligand, and a protein. Predicting the strength of protein-ligand binding with…