Related papers: GPU-Accelerated Drug Discovery with Docking on the…

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…

This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition. The prediction of protein-ligand binding regions is an active research domain in computational biophysics and…

Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…

The COVID-19 pandemic has led to unprecedented efforts to identify drugs that can reduce its associated morbidity/mortality rate. Computational chemistry approaches hold the potential for triaging potential candidates far more quickly than…

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…

The machine learning (ML) and deep learning (DL) techniques are widely recognized to be powerful tools for virtual drug screening. The recently reported ML- or DL-based scoring functions have shown exciting performance in predicting…

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can…

Scaffold based drug discovery (SBDD) is a technique for drug discovery which pins chemical scaffolds as the framework of design. Scaffolds, or molecular frameworks, organize the design of compounds into local neighborhoods. We formalize…

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-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…

Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-efficient, search-based docking framework…

DNA-Encoded Library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially-generated molecular libraries. DEL screens measure protein binding affinity though sequencing reads…

There remains an urgent need to identify existing drugs that might be suitable for treating patients suffering from COVID-19 infection. Drugs rarely act at a single molecular target, with off target effects often being responsible for…

Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…

Due to SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) being a novel virus, there are currently no known effective antiviral drugs capable of slowing its progress. To accelerate the discovery of potential drug candidates,…

The heterogeneous computing paradigm has led to the need for portable and efficient programming solutions that can leverage the capabilities of various hardware devices, such as NVIDIA, Intel, and AMD GPUs. This study evaluates the…

We present results of testing of the ability of eleven popular scoring functions to predict native docked positions using a recently developed method [1] for estimation the entropy contributions of relative motions to protein-ligand binding…

SkeleDock is a scaffold docking algorithm which uses the structure of a protein-ligand complex as a template to model the binding mode of a chemically similar system. This algorithm was evaluated in the D3R Grand Challenge 4 pose prediction…

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…

Structure-based virtual screening (SBVS) is a promising in silico technique that integrates computational methods into drug design. An extensively used method in SBVS is molecular docking. However, the docking process can hardly be…