Journal of chemical information and modeling
Apr 8, 2015
Molecular docking, despite its undeniable usefulness in computer-aided drug design protocols and the increasing sophistication of tools used in the prediction of ligand-protein interaction energies, is still connected with a problem of effective resu...
Computational intelligence and neuroscience
Mar 22, 2015
Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the f...
BACKGROUND: Accurately predicting the binding affinities of large sets of protein-ligand complexes is a key challenge in computational biomolecular science, with applications in drug discovery, chemical biology, and structural biology. Since a scorin...
OBJECTIVE: The objective of this paper is to highlight the state-of-the-art machine learning (ML) techniques in computational docking. The use of smart computational methods in the life cycle of drug design is relatively a recent development that has...
Journal of chemical information and modeling
Feb 9, 2015
The pharmacophore concept is commonly employed in virtual screening for hit identification. A pharmacophore is generally defined as the three-dimensional arrangement of the structural and physicochemical features of a compound responsible for its aff...
The study of biomolecular interactions between a drug and its biological target is of paramount importance for the design of novel bioactive compounds. In this paper, we report on the use of molecular dynamics (MD) simulations and machine learning to...
Journal of computer-aided molecular design
Dec 20, 2014
The assessment of binding affinity between ligands and the target proteins plays an essential role in drug discovery and design process. As an alternative to widely used scoring approaches, machine learning methods have also been proposed for fast pr...
Ligand-based drug discovery methods typically utilize pharmacophore similarities among molecules to screen for potential active compounds. Among these, scaffold hopping is a widely used ligand-based lead identification strategy that facilitates clini...
Journal of molecular graphics & modelling
Sep 1, 2025
Parkinson's disease is a neurodegenerative condition that affects the brain's neurons, and causes malfunction of nerve cells and their death. A neurotransmitter called dopamine interacts with the part of the brain in charge of coordination and moveme...
In the histone deacetylase (HDAC) family, HDAC11 is the smallest and a single member under the class IV subtype. It is important as a drug target mainly in cancer, inflammatory and autoimmune diseases. The design and development of selective HDAC11 i...
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