Related papers: MC-GNNAS-Dock: Multi-criteria GNN-based Algorithm …

Learning-to-rank, a machine learning technique widely used in information retrieval, has recently been applied to the problem of ligand-based virtual screening, to accelerate the early stages of new drug development. Ranking prediction…

Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…

We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA…

Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…

Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must…

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.…

Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…

Automated vehicles and logistics robots must often position themselves in narrow environments with high precision in front of a specific target, such as a package or their charging station. Often, these docking scenarios are solved in two…

Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent…

We present the Multiple Criteria Decision Analysis Methods Selection Software (MCDA-MSS). This decision support system helps analysts answering a recurring question in decision science: Which is the most suitable Multiple Criteria Decision…

Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational…

Determinantal point processes (DPPs) are an elegant model for encoding probabilities over subsets, such as shopping baskets, of a ground set, such as an item catalog. They are useful for a number of machine learning tasks, including product…

Neural architecture search (NAS) methods aim to automatically find the optimal deep neural network (DNN) architecture as measured by a given objective function, typically some combination of task accuracy and inference efficiency. For many…

Molecular property prediction (MPP) is a fundamental but challenging task in the computer-aided drug discovery process. More and more recent works employ different graph-based models for MPP, which have made considerable progress in…

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance…

Neural architecture search (NAS) has gained significant traction in automating the design of neural networks. To reduce search time, differentiable architecture search (DAS) reframes the traditional paradigm of discrete candidate sampling…

Molecular docking is a structure-based computational drug design technique for predicting the interaction between a small molecule (ligand) and a macromolecule (receptor). Over the past three decades various docking software programs have…

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding…

Predicting the properties of a molecule from its structure is a challenging task. Recently, deep learning methods have improved the state of the art for this task because of their ability to learn useful features from the given data. By…

Modern advances in machine learning (ML) and wearable medical sensors (WMSs) in edge devices have enabled ML-driven disease detection for smart healthcare. Conventional ML-driven methods for disease detection rely on customizing individual…