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In recent years, machine learning has been proposed as a promising strategy to build accurate scoring functions for computational docking finalized to numerically empowered drug discovery. However, the latest studies have suggested that…

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…

Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…

Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has…

Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because…

This study assesses the efficiency of several popular machine learning approaches in the prediction of molecular binding affinity: CatBoost, Graph Attention Neural Network, and Bidirectional Encoder Representations from Transformers. The…

Assessing drug-target affinity is a critical step in the drug discovery and development process, but to obtain such data experimentally is both time consuming and expensive. For this reason, computational methods for predicting binding…

The training set of atomic configurations is key to the performance of any Machine Learning Force Field (MLFF) and, as such, the training set selection determines the applicability of the MLFF model for predictive molecular simulations.…

A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…

The primary objective of most lead optimization campaigns is to enhance the binding affinity of ligands. For large molecules such as antibodies, identifying mutations that enhance antibody affinity is particularly challenging due to the…

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…

Building robust deep learning-based models requires large quantities of diverse training data. In this study, we investigate the use of federated learning (FL) to build medical imaging classification models in a real-world collaborative…

Accurate prediction of protein-ligand binding affinities is crucial for drug development. Recent advances in machine learning show promising results on this task. However, these methods typically rely heavily on labeled data, which can be…

This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology…

The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different explanatory factors of variation behind…

Modern ML systems increasingly augment input instances with additional relevant information to enhance final prediction. Despite growing interest in such retrieval-augmented models, their fundamental properties and training are not well…

Software fault prediction (SFP) is a critical task in software engineering, enabling early identification of faults in modules to improve software quality and reduce maintenance costs. This research investigates the combined effects of…

Meta-learning algorithms aim to learn two components: a model that predicts targets for a task, and a base learner that quickly updates that model when given examples from a new task. This additional level of learning can be powerful, but…

Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. This study evaluates the performance of…

Though data augmentation has become a standard component of deep neural network training, the underlying mechanism behind the effectiveness of these techniques remains poorly understood. In practice, augmentation policies are often chosen…