International journal of molecular sciences
Nov 25, 2021
Chemical compounds can be represented as attributed graphs. An attributed graph is a mathematical model of an object composed of two types of representations: nodes and edges. Nodes are individual components, and edges are relations between these com...
Resistance to small-molecule drugs is the main cause of the failure of therapeutic drugs in clinical practice. Missense mutations altering the binding of ligands to proteins are one of the critical mechanisms that result in genetic disease and drug r...
Journal of chemical information and modeling
Nov 18, 2021
In recent years, deep learning-based methods have emerged as promising tools for drug design. Most of these methods are ligand-based, where an initial target-specific ligand data set is necessary to design potent molecules with optimized properties....
BACKGROUND: Accurate prediction of protein-ligand binding affinity is important for lowering the overall cost of drug discovery in structure-based drug design. For accurate predictions, many classical scoring functions and machine learning-based meth...
BACKGROUND: Recently, machine learning-based ligand activity prediction methods have been greatly improved. However, if known active compounds of a target protein are unavailable, the machine learning-based method cannot be applied. In such cases, do...
Journal of computer-aided molecular design
Oct 28, 2021
The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to biological macromolecules has far-re...
International journal of molecular sciences
Oct 26, 2021
Olfactory receptors (ORs) constitute the largest superfamily of G protein-coupled receptors (GPCRs). ORs are involved in sensing odorants as well as in other ectopic roles in non-nasal tissues. Matching of an enormous number of the olfactory stimulat...
Journal of chemical information and modeling
Oct 15, 2021
One of the main challenges of structure-based virtual screening (SBVS) is the incorporation of the receptor's flexibility, as its explicit representation in every docking run implies a high computational cost. Therefore, a common alternative to inclu...
Microtubules are receiving enormous interest in drug discovery due to the important roles they play in cellular functions. Targeting tubulin polymerization presents an excellent opportunity for the development of anti-tubulin drugs. Drug resistance a...
The MANORAA platform uses structure-based approaches to provide information on drug design originally derived from mapping tens of thousands of amino acids on a grid. In-depth analyses of the pockets, frequently occurring atoms, influential distances...