Journal of chemical theory and computation
Feb 25, 2022
Understanding the process of ligand-protein recognition is important to unveil biological mechanisms and to guide drug discovery and design. Enhanced-sampling molecular dynamics is now routinely used to simulate the ligand binding process, resulting ...
Drug discovery pipelines typically involve high-throughput screening of large amounts of compounds in a search of potential drugs candidates. As a chemical space of small organic molecules is huge, a "navigation" over it urges for fast and lightweigh...
Journal of biomolecular structure & dynamics
Feb 23, 2022
The development of new drugs against is an essential strategy for fighting drug resistance. Although 3-dehydroquinate dehydratase (MtDHQ) is known to be a highly relevant target for , current research shows new putative inhibitors of MtDHQ selected ...
Journal of chemical theory and computation
Feb 23, 2022
The determination of drug residence times, which define the time an inhibitor is in complex with its target, is a fundamental part of the drug discovery process. Synthesis and experimental measurements of kinetic rate constants are, however, expensiv...
Internalin B-mediated activation of the membrane-bound receptor tyrosine kinase MET is accompanied by a change in receptor mobility. Conversely, it should be possible to infer from receptor mobility whether a cell has been treated with internalin B. ...
With the recent explosion of chemical libraries beyond a billion molecules, more efficient virtual screening approaches are needed. The Deep Docking (DD) platform enables up to 100-fold acceleration of structure-based virtual screening by docking onl...
Journal of chemical information and modeling
Feb 4, 2022
Fast and accurate assessment of small-molecule dihedral energetics is crucial for molecular design and optimization in medicinal chemistry. Yet, accurate prediction of torsion energy profiles remains challenging as the current molecular mechanics (MM...
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2022
Computational drug design relies on the calculation of binding strength between two biological counterparts especially a chemical compound, i.e., a ligand, and a protein. Predicting the affinity of protein-ligand binding with reasonable accuracy is c...
Current opinion in structural biology
Jan 31, 2022
The success of Artificial Intelligence (AI) across a wide range of domains has fuelled significant interest in its application to designing novel compounds and screening compounds against a specific target. However, many existing AI methods either do...
BACKGROUND: Alkaline earth metal ions are important protein binding ligands in human body, and it is of great significance to predict their binding residues.