Journal of chemical information and modeling
Jul 17, 2023
Identifying compound-protein interactions (CPIs) is crucial for drug discovery. Since experimentally validating CPIs is often time-consuming and costly, computational approaches are expected to facilitate the process. Rapid growths of available CPI d...
Phosphorylation is one of the most important post-translational modifications and plays a pivotal role in various cellular processes. Although there exist several computational tools to predict phosphorylation sites, existing tools have not yet harne...
Predicting peptide detectability is useful in a variety of mass spectrometry (MS)-based proteomics applications, particularly targeted proteomics. However, most machine learning-based computational methods have relied solely on information from the p...
Chembiochem : a European journal of chemical biology
Jul 12, 2023
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical re...
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...
International journal of biological macromolecules
Jul 4, 2023
The identification of antioxidant proteins is a challenging yet meaningful task, as they can protect against the damage caused by some free radicals. In addition to time-consuming, laborious, and expensive experimental identification methods, efficie...
Journal of chemical information and modeling
Jul 3, 2023
Determining the catalytic site of enzymes is a great help for understanding the relationship between protein sequence, structure, and function, which provides the basis and targets for designing, modifying, and enhancing enzyme activity. The unique l...
Proceedings of the National Academy of Sciences of the United States of America
Jul 3, 2023
The CASP14 experiment demonstrated the extraordinary structure modeling capabilities of artificial intelligence (AI) methods. That result has ignited a fierce debate about what these methods are actually doing. One of the criticisms has been that the...
The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallogr...
Current opinion in structural biology
Jun 28, 2023
Recently, prediction of structural/functional motifs in protein sequences takes advantage of powerful machine learning based approaches. Protein encoding adopts protein language models overpassing standard procedures. Different combinations of machin...
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