Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelera...
Current opinion in structural biology
Feb 13, 2024
Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional sites. The advantages of allosteric modulators over orthosteric ones have sparked t...
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI)...
The rank ordering of ligands remains one of the most attractive challenges in drug discovery. While physics-based in silico binding affinity methods dominate the field, they still have problems, which largely revolve around forcefield accuracy and sa...
Understanding the mechanisms of protein-DNA binding is critical in comprehending gene regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key role in these mechanisms. In this study, we present a deep learning-based meth...
Protein-protein interactions (PPIs) are pivotal for driving diverse biological processes, and any disturbance in these interactions can lead to disease. Thus, the study of PPIs has been a central focus in biology. Recent developments in deep learning...
The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones ...
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a s...
Proceedings of the National Academy of Sciences of the United States of America
Feb 1, 2024
Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure from sequence, determining protein function from its sequence or struct...
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO famili...
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