Results 1 to 10 of about 4,190,416 (396)
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking [PDF]
arXiv, 2022 Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy.
Gabriele Corso +4 more
arxiv +3 more sources
Do Deep Learning Models Really Outperform Traditional Approaches in Molecular Docking? [PDF]
arXiv, 2023 Molecular docking, given a ligand molecule and a ligand binding site (called ``pocket'') on a protein, predicting the binding mode of the protein-ligand complex, is a widely used technique in drug design. Many deep learning models have been developed for molecular docking, while most existing deep learning models perform docking on the whole protein ...
Yuejiang Yu +4 more
arxiv +3 more sources
Scientific Reports, 2023 Molecular docking is a computational technique that predicts the binding affinity of ligands to receptor proteins. Although it has potential uses in nutraceutical research, it has developed into a formidable tool for drug development.
P. Agu +7 more
semanticscholar +2 more sources
Highly flexible protein-peptide docking using CABS-dock [PDF]
Ora Schueler-Furman and Nir London (eds.), Modeling
Peptide-Protein Interactions: Methods and Protocols, Methods in Molecular
Biology, vol. 1561, 2017, 2016 Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking.
Ciemny, Maciej Pawel +4 more
arxiv +3 more sources
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design [PDF]
arXiv, 2021 The field of machine learning for drug discovery is witnessing an explosion of novel methods. These methods are often benchmarked on simple physicochemical properties such as solubility or general druglikeness, which can be readily computed. However, these properties are poor representatives of objective functions in drug design, mainly because they do
Miguel Garc'ia-Orteg'on +5 more
arxiv +3 more sources
The Art and Science of Molecular Docking
Annual Review of BiochemistryMolecular docking has become an essential part of a structural biologist's and medicinal chemist's toolkits. Given a chemical compound and the three-dimensional structure of a molecular target—for example, a protein—docking methods fit the compound into the target, predicting the compound's bound structure and binding energy.
Joseph M, Paggi +2 more
openaire +3 more sources
GNINA 1.0: molecular docking with deep learning
Journal of Cheminformatics, 2021 Molecular docking computationally predicts the conformation of a small molecule when binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline as they determine the fitness of sampled poses.
Andrew T. McNutt +7 more
semanticscholar +1 more source
Frontiers in Pharmacology, 2023 Objective: Curcumin is a plant polyphenol extracted from the Chinese herb turmeric. It was found that curcumin has good anti-cancer properties in a variety of cancers, but the exact mechanism is not clear.
Qingmin He +7 more
semanticscholar +1 more source
International Journal of Molecular Sciences, 2023 The use of deer antlers dates back thousands of years in Chinese history. Deer antlers have antitumor, anti-inflammatory, and immunomodulatory properties and can be used in treating neurological diseases.
Lingyu Liu +5 more
semanticscholar +1 more source
Molecular docking in organic, inorganic, and hybrid systems: a tutorial review
Chemical Monthly, 2023 Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA,
Madhuchhanda Mohanty, P. Mohanty
semanticscholar +1 more source