INTRODUCTION: Antibody-mediated immunity is an essential part of the immune system in vertebrates. The ability to specifically bind to antigens allows antibodies to be widely used in the therapy of cancers and other critical diseases. A key step in a...
BACKGROUND: Compound-protein interaction site and binding affinity predictions are crucial for drug discovery and drug design. In recent years, many deep learning-based methods have been proposed for predications related to compound-protein interacti...
Journal of bioinformatics and computational biology
Dec 14, 2022
In this study, we propose , a system that aims to computationally generate novel antiviral peptides (AVPs). This system relies on the key premise of the Generative Adversarial Network (GAN) model and the Feedback method. GAN, a generative modeling ap...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Essential proteins are considered the foundation of life as they are indispensable for the survival of living organisms. Computational methods for essential protein discovery provide a fast way to identify essential proteins. But most of them heavily...
BACKGROUND: Protein-protein interactions are widespread in biological systems and play an important role in cell biology. Since traditional laboratory-based methods have some drawbacks, such as time-consuming, money-consuming, etc., a large number of...
The ubiquitous availability of genome sequencing data explains the popularity of machine learning-based methods for the prediction of protein properties from their amino acid sequences. Over the years, while revising our own work, reading submitted m...
Machine learning and in particular deep learning (DL) are increasingly important in mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention time, ion mobility and fragment intensities of a peptide just from the amino acid ...
The prediction of mechanical and dynamical properties of proteins is an important frontier, especially given the greater availability of proteins structures. Here we report a series of models that provide end-to-end predictions of nanodynamical prope...
BACKGROUND: Analysis of the distribution of amino acid types found at equivalent positions in multiple sequence alignments has found applications in human genetics, protein engineering, drug design, protein structure prediction, and many other fields...
Interdisciplinary sciences, computational life sciences
Nov 8, 2022
PURPOSE: The determination of which amino acid in a protein interacts with other proteins is important in understanding the functional mechanism of that protein. Although there are experimental methods to detect protein-protein interaction sites (PPI...