IEEE/ACM transactions on computational biology and bioinformatics
Apr 1, 2022
Attention mechanism has the ability to find important information in the sequence. The regions of the RNA sequence that can bind to proteins are more important than those that cannot bind to proteins. Neither conventional methods nor deep learning-ba...
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...
Computational approaches for predicting protein-protein interfaces are extremely useful for understanding and modelling the quaternary structure of protein assemblies. In particular, partner-specific binding site prediction methods allow delineating ...
Structure-based pharmacophore models are often developed by selecting a single protein-ligand complex with good resolution and better binding affinity data which prevents the analysis of other structures having a similar potential to act as better te...
Genomics, proteomics & bioinformatics
Mar 12, 2022
Although computational approaches have been complementing high-throughput biological experiments for the identification of functional regions in the human genome, it remains a great challenge to systematically decipher interactions between transcript...
Accurate prediction of binding poses is crucial to structure-based drug design. We employ two powerful artificial intelligence (AI) approaches, data-mining and machine-learning, to design artificial neural network (ANN) based pose-scoring function. I...
Transcription factors (TFs) play an important role in regulating gene expression, thus the identification of the sites bound by them has become a fundamental step for molecular and cellular biology. In this paper, we developed a deep learning framewo...
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 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...
Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts...