Treatment of COVID-19 with a soluble version of ACE2 that binds to SARS-CoV-2 virions before they enter host cells is a promising approach, however it needs to be optimized and adapted to emerging viral variants. The computational workflow presented ...
Protein-protein interactions play a ubiquitous role in biological function. Knowledge of the three-dimensional (3D) structures of the complexes they form is essential for understanding the structural basis of those interactions and how they orchestra...
Current sequence-based predictors of protein-binding residues (PBRs) belong to two distinct categories: structure-trained vs. intrinsic disorder-trained. Since disordered PBRs differ from structured PBRs in several ways, including ability to bind mul...
Machine learning (ML) applications have become ubiquitous in all fields of research including protein science and engineering. Apart from protein structure and mutation prediction, scientists are focusing on knowledge gaps with respect to the molecul...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Identification of transcription factor binding sites (TFBSs) is essential for revealing the rules of protein-DNA binding. Although some computational methods have been presented to predict TFBSs using epigenomic and sequence features, most of them ig...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Protein-DNA interactions play an important role in diverse biological processes. Accurately identifying protein-DNA binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental me...
Journal of chemical information and modeling
Nov 7, 2022
Molecular docking tools are regularly used to computationally identify new molecules in virtual screening for drug discovery. However, docking tools suffer from inaccurate scoring functions with widely varying performance on different proteins. To en...
Journal of chemical information and modeling
Nov 7, 2022
The analysis and comparison of protein-binding sites aid various applications in the drug discovery process, e.g., hit finding, drug repurposing, and polypharmacology. Classification of binding sites has been a hot topic for the past 30 years, and ma...
The number of SARS-CoV-2 spike Receptor Binding Domain (RBD) with multiple amino acid mutations is huge due to random mutations and combinatorial explosions, making it almost impossible to experimentally determine their binding affinities to human an...
Journal of chemical information and modeling
Oct 21, 2022
In structure-based virtual screening (SBVS), it is critical that scoring functions capture protein-ligand atomic interactions. By focusing on the local domains of ligand binding pockets, a standardized pocket Pfam-based clustering (Pfam-cluster) appr...
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