There has been considerable recent progress in designing new proteins using deep-learning methods. Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de no...
Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X...
The global outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 virus had led to profound respiratory health implications. This study focused on designing organoselenium-based inhibitors targeting the SARS-CoV-2 main protease (M). The ligand-bi...
Protein science : a publication of the Protein Society
38717278
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragm...
Annotating active sites in enzymes is crucial for advancing multiple fields including drug discovery, disease research, enzyme engineering, and synthetic biology. Despite the development of numerous automated annotation algorithms, a significant trad...
Proceedings of the National Academy of Sciences of the United States of America
39589882
Machine learning (ML) is transforming the investigation of complex biological processes. In enzymatic catalysis, one significant challenge is identifying the reactive conformations (RC) of the enzyme:substrate complex where the substrate assumes a pr...
The accurate identification of catalytic residues contributes to our understanding of enzyme functions in biological processes and pathways. The increasing number of protein sequences necessitates computational tools for the automated prediction of c...
Journal of chemical information and modeling
39928564
Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes reve...
International journal of molecular sciences
40243651
In this study, we utilized machine learning techniques to identify potential inhibitors of the MERS-CoV 3CL protease. Among the models evaluated, the Random Forest (RF) algorithm exhibited the highest predictive performance, achieving an accuracy of ...
Cytochrome P450 1A2, as many isoenzymes, can generate multiple metabolites from a single substrate. A loose coupling between substrate binding and oxygen activation makes possible substrate reorientations at the active site prior to catalysis. In the...