Journal of molecular graphics & modelling
Jun 18, 2018
Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques c...
High-performance ligand-based virtual screening (VS) models have been developed using various computational methods, including the deep neural network (DNN) method. There are high expectations for exploration of the advanced capabilities of DNN to im...
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions...
Protein kinases are dynamic, adopting different conformational states that are critical for their catalytic activity. We assess a range of structural features derived from the conserved αC helix and DFG motif to define the conformational space of the...
The identification of subtype-selective GPCR (G-protein coupled receptor) ligands is a challenging task. In this study, we developed a computational protocol to find compounds with 5-HTR versus 5-HTR selectivity. Our approach employs the hierarchical...
Journal of chemical information and modeling
May 8, 2018
Undetected overfitting can occur when there are significant redundancies between training and validation data. We describe AVE, a new measure of training-validation redundancy for ligand-based classification problems, that accounts for the similarity...
The journal of physical chemistry letters
Apr 17, 2018
Predicting the activity of chemicals for a given odorant receptor is a longstanding challenge. Here the activity of 258 chemicals on the human G-protein-coupled odorant receptor (OR)51E1, also known as prostate-specific G-protein-coupled receptor 2 (...
Journal of chemical information and modeling
Feb 22, 2018
Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geomet...
Current opinion in structural biology
Feb 20, 2018
Data driven computational approaches to predicting protein-ligand binding are currently achieving unprecedented levels of accuracy on held-out test datasets. Up until now, however, this has not led to corresponding breakthroughs in our ability to des...