Nowadays, multiple solutions are known for identifying ligand-protein binding sites. Another important task is labeling each point of a binding site with the appropriate atom type, a process known as pseudo-ligand generation. The number of solutions ...
Peptides are gaining significant attention in diverse fields such as the pharmaceutical market has seen a steady rise in peptide-based therapeutics over the past six decades. Peptides have been utilized in the development of distinct applications inc...
Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations...
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
BACKGROUND: A massive amount of protein sequences have been obtained, but their functions remain challenging to discern. In recent research on protein function prediction, Protein-Protein Interaction (PPI) Networks have played a crucial role. Uncover...
O-linked glycosylation is a crucial post-translational modification that regulates protein function and biological processes. Dysregulation of this process is associated with various diseases, underscoring the need to accurately identify O-linked gly...
Journal of chemical theory and computation
Jan 30, 2025
Despite its importance in understanding biology and computer-aided drug discovery, the accurate prediction of protein ionization states remains a formidable challenge. Physics-based approaches struggle to capture the small, competing contributions in...
Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures ...
Computational target identification plays a pivotal role in the drug development process. With the significant advancements of deep learning methods for protein structure prediction, the structural coverage of human proteome has increased substantial...
Template-based modelling, also known as homology modelling, is a powerful approach to predict the structure of a protein from its amino acid sequence. The approach requires one to identify a sequence similarity between the query sequence and that of ...
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