International journal of molecular sciences
Nov 18, 2023
Machine learning has been increasingly utilized in the field of protein engineering, and research directed at predicting the effects of protein mutations has attracted increasing attention. Among them, so far, the best results have been achieved by r...
CONTEXT: Machine learning techniques are becoming increasingly important in the selection and optimization of therapeutic molecules, as well as for the selection of formulation components and the prediction of long-term stability. Compared to first-p...
Functional annotation of open reading frames in microbial genomes remains substantially incomplete. Enzymes constitute the most prevalent functional gene class in microbial genomes and can be described by their specific catalytic functions using the ...
AlphaFold2 (ref. ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates, and disease-causing point mutations often ca...
Journal of chemical information and modeling
Nov 13, 2023
Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. H...
BACKGROUND: Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Predict...
Journal of chemical theory and computation
Nov 8, 2023
Flexible modeling of the protein-ligand complex structure is a fundamental challenge for in silico drug development. Recent studies have improved commonly used docking tools by incorporating extra-deep learning-based steps. However, such strategies l...
Journal of chemical information and modeling
Nov 6, 2023
Phosphorylation, as one of the most important post-translational modifications, plays a key role in various cellular physiological processes and disease occurrences. In recent years, computer technology has been gradually applied to the prediction of...
Acta crystallographica. Section D, Structural biology
Nov 3, 2023
Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedu...
Chemical proteomics utilizes small-molecule probes to covalently engage with their interacting proteins. Since chemical probes are tagged to the active or binding sites of functional proteins, chemical proteomics can be used to profile protein target...