IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
Protein Secondary Structural Class (PSSC) information is important in investigating further challenges of protein sequences like protein fold recognition, protein tertiary structure prediction, and analysis of protein functions for drug discovery. Id...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
The discovery of potential Drug-Target Interactions (DTIs) is a determining step in the drug discovery and repositioning process, as the effectiveness of the currently available antibiotic treatment is declining. Although putting efforts on the tradi...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
Knowledge of protein functions plays an important role in biology and medicine. With the rapid development of high-throughput technologies, a huge number of proteins have been discovered. However, there are a great number of proteins without function...
There has been considerable recent progress in protein structure prediction using deep neural networks to predict inter-residue distances from amino acid sequences. Here we investigate whether the information captured by such networks is sufficiently...
Identifying potential associations between proteins and compounds is significant and challenging in the drug discovery process. Existing deep-learning-based methods tend to treat compounds and proteins as sequences or graphs. Inspired by the rapid de...
International journal of molecular sciences
Nov 28, 2021
In silico protein-ligand binding prediction is an ongoing area of research in computational chemistry and machine learning based drug discovery, as an accurate predictive model could greatly reduce the time and resources necessary for the detection a...
International journal of molecular sciences
Nov 27, 2021
The field of protein structure prediction has recently been revolutionized through the introduction of deep learning. The current state-of-the-art tool AlphaFold2 can predict highly accurate structures; however, it has a prohibitively long inference ...
Architected biomaterials, as well as sound and music, are constructed from small building blocks that are assembled across time- and length-scales. Here we present a novel deep learning-enabled integrated algorithmic workflow to merge the two concept...
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...
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...