Related papers: Parallel multi-objective algorithms for the molecu…

Despite the great popularity of virtual screening of existing compound libraries, the search for new potential drug candidates also takes advantage of generative protocols, where new compound suggestions are enumerated using various…

Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide…

Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of classical algorithms have been developed to carry out…

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…

Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…

The field of machine learning for drug discovery is witnessing an explosion of novel methods. These methods are often benchmarked on simple physicochemical properties such as solubility or general druglikeness, which can be readily…

Gaussian Boson Samplers are photonic quantum devices with the potential to perform tasks that are intractable for classical systems. As with other near-term quantum technologies, an outstanding challenge is to identify specific problems of…

In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase…

Molecular discovery is a multi-objective optimization problem that requires identifying a molecule or set of molecules that balance multiple, often competing, properties. Multi-objective molecular design is commonly addressed by combining…

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

Many real-world applications require decision-makers to assess the quality of solutions while considering multiple conflicting objectives. Obtaining good approximation sets for highly constrained many-objective problems is often a difficult…

To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

Molecular docking is a major element in drug discovery and design. It enables the prediction of ligand-protein interactions by simulating the binding of small molecules to proteins. Despite the availability of numerous docking algorithms,…

Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…

Molecular docking (MD) is a crucial task in drug design, which predicts the position, orientation, and conformation of the ligand when bound to a target protein. It can be interpreted as a combinatorial optimization problem, where quantum…

Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…

Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric…