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Journal of chemical information and modeling
Feb 22, 2024
Developing new drugs is too expensive and time -consuming. Accurately predicting the interaction between drugs and targets will likely change how the drug is discovered. Machine learning-based protein-ligand interaction prediction has demonstrated si...
Nature communications
Feb 22, 2024
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at in...
Journal of chemical information and modeling
Feb 17, 2024
Predicting the binding affinity of protein-ligand complexes is crucial for computer-aided drug discovery (CADD) and the identification of potential drug candidates. The deep learning-based scoring functions have emerged as promising predictors of bin...
Molecular informatics
Feb 15, 2024
When designing a machine learning-based scoring function, we access a limited number of protein-ligand complexes with experimentally determined binding affinity values, representing only a fraction of all possible protein-ligand complexes. Consequent...
Nature biotechnology
Feb 15, 2024
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...
Molecules (Basel, Switzerland)
Feb 13, 2024
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)...
Molecules (Basel, Switzerland)
Feb 13, 2024
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...
Nature communications
Feb 9, 2024
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...
Current opinion in structural biology
Feb 7, 2024
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...