Related papers: Dockformer: A transformer-based molecular docking …

Drug discovery is the most expensive, time demanding and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should…

High-throughput approximations of quantum mechanics calculations and combinatorial experiments have been traditionally used to reduce the search space of possible molecules, drugs and materials. However, the interplay of structural and…

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…

In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…

In this work, we propose a novel deep online correction (DOC) framework for monocular visual odometry. The whole pipeline has two stages: First, depth maps and initial poses are obtained from convolutional neural networks (CNNs) trained in…

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the…

Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing challenges for…

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…

Identifying protein targets for small molecules, or reverse screening, is essential for understanding drug action, guiding compound repurposing, predicting off-target effects, and elucidating the molecular mechanisms of bioactive compounds.…

Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…

Deep-predictive-coding networks (DPCNs) are hierarchical, generative models. They rely on feed-forward and feed-back connections to modulate latent feature representations of stimuli in a dynamic and context-sensitive manner. A crucial…

Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in…

Monocular depth estimation is a fundamental task in computer vision and has drawn increasing attention. Recently, some methods reformulate it as a classification-regression task to boost the model performance, where continuous depth is…

CXCR7, a G-protein-coupled chemokine receptor, has recently emerged as a key player in cancer progression, particularly in driving angiogenesis and metastasis. Despite its significance, currently, few effective inhibitors exist for…

Docking is an important tool in computational drug discovery that aims to predict the binding pose of a ligand to a target protein through a combination of pose scoring and optimization. A scoring function that is differentiable with…

New computational strategies, such as molecular docking, are emerging to speed up the drug discovery process. This method predicts the activity of molecules at the binding site of proteins, helping to select the ones that exhibit desirable…

While transformers have shown great potential on video recognition with their strong capability of capturing long-range dependencies, they often suffer high computational costs induced by the self-attention to the huge number of 3D tokens.…

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…