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Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by…
Molecular docking is a crucial phase in drug discovery, involving the precise determination of the optimal spatial arrangement between two molecules when they bind. The such analysis, the 3D structure of molecules is a fundamental…
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.…
Accurately predicting the binding conformation of small-molecule ligands to protein targets is a critical step in rational drug design. Although recent deep learning-based docking surpasses traditional methods in speed and accuracy, many…
Molecular Docking (MD) is an important step of the drug discovery process which aims at calculating the preferred position and shape of one molecule to a second when they are bound to each other. During such analysis, 3D representations of…
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…
The D-Wave quantum annealers make it possible to obtain high quality solutions of NP-hard problems by mapping a problem in a QUBO (quadratic unconstrained binary optimization) or Ising form to the physical qubit connectivity structure on…
Molecular docking is a critical computational method in drug discovery used to predict the binding conformation and orientation of a ligand within a protein's binding site. Mapping this challenge onto a graph-based problem, specifically the…
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…
Modern quantum annealers can find high-quality solutions to combinatorial optimisation objectives given as quadratic unconstrained binary optimisation (QUBO) problems. Unfortunately, obtaining suitable QUBO forms in computer vision remains…
Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…
In silico de novo design can drastically cut the costs and time of drug development. In particular, a key advantage of bottom-up physics-based approaches is their independence from training datasets, unlike generative models. However, they…
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…
Predicting the docking between proteins and ligands is a crucial and challenging task for drug discovery. However, traditional docking methods mainly rely on scoring functions, and deep learning-based docking approaches usually neglect the…
Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structure-function relationship, predict molecular function, or design new drugs. Results: We explore a new approach for ligand prediction in…
In this work, we explore graph partitioning (GP) using quantum annealing on the D-Wave 2X machine. Motivated by a recently proposed graph-based electronic structure theory applied to quantum molecular dynamics (QMD) simulations, graph…
Quantum annealing provides a promising route for the development of quantum optimization devices, but the usefulness of such devices will be limited in part by the range of implementable problems as dictated by hardware constraints. To…
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…