Journal of computer-aided molecular design
Aug 26, 2022
Molecular visualization is a cornerstone of structural biology, providing insights into the form and function of biomolecules that are difficult to achieve any other way. Scientific analysis, publication, education, and outreach often benefit from ph...
Journal of computer-aided molecular design
May 27, 2022
Optimization of compound metabolic stability is a highly topical issue in pharmaceutical research. Accordingly, application of predictive in silico models can potentially reduce the number of design-make-test-analyze iterations and consequently speed...
Journal of computer-aided molecular design
Mar 29, 2022
The retrospective evaluation of virtual screening approaches and activity prediction models are important for methodological development. However, for fair comparison, evaluation data sets must be carefully prepared. In this research, we compiled str...
Journal of computer-aided molecular design
Mar 22, 2022
Modern molecular docking comprises the prediction of pose and affinity. Prediction of docking poses is required for affinity prediction when three-dimensional coordinates of the ligand have not been provided. However, a large number of feature engine...
Journal of computer-aided molecular design
Mar 19, 2022
The support vector machine (SVM) algorithm is one of the most widely used machine learning (ML) methods for predicting active compounds and molecular properties. In chemoinformatics and drug discovery, SVM has been a state-of-the-art ML approach for ...
Journal of computer-aided molecular design
Jan 21, 2022
Nowadays, activity prediction is key to understanding the mechanism-of-action of active structures discovered from phenotypic screening or found in natural products. Machine learning is currently one of the most important and rapidly evolving topics ...
Journal of computer-aided molecular design
Nov 24, 2021
We here present a streamlined, explainable graph convolutional neural network (gCNN) architecture for small molecule activity prediction. We first conduct a hyperparameter optimization across nearly 800 protein targets that produces a simplified gCNN...
Journal of computer-aided molecular design
Oct 30, 2021
Predicting the sensory properties of compounds is challenging due to the subjective nature of the experimental measurements. This testing relies on a panel of human participants and is therefore also expensive and time-consuming. We describe the appl...
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...
Journal of computer-aided molecular design
Oct 8, 2021
Fast and accurate identification of inhibitors with potency against HCV NS5B polymerase is currently a challenging task. As conventional experimental methods is the gold standard method for the design and development of new HCV inhibitors, they often...