Journal of chemical theory and computation
Jan 11, 2024
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expandi...
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Jan 10, 2024
One of the main challenges in small molecule drug discovery is finding novel chemical compounds with desirable activity. Traditional drug development typically begins with target selection, but the correlation between targets and disease remains to b...
Journal of chemical information and modeling
Jan 7, 2024
A central problem in drug discovery is to identify the interactions between drug-like compounds and protein targets. Over the past few decades, various quantitative structure-activity relationship (QSAR) and proteo-chemometric (PCM) approaches have b...
AlphaFold, an artificial intelligence (AI)-based tool for predicting the 3D structure of proteins, is now widely recognized for its high accuracy and versatility in the folding of human proteins. AlphaFold is useful for understanding structure-functi...
Serine phosphorylation plays a pivotal role in the pathogenesis of various cellular processes and diseases. Roughly 81% of human diseases have links to phosphorylation, and an overwhelming 86.4% of protein phosphorylation takes place at serine residu...
Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single- and multichain multiple-sequence alignment (MSA) construction. Large-scale benchmarks show that DeepM...
Journal of chemical information and modeling
Jan 2, 2024
Protein thermodynamic stability is essential to clarify the relationships among structure, function, and interaction. Therefore, developing a faster and more accurate method to predict the impact of the mutations on protein stability is helpful for p...
Ligand docking (LD), a technology for predicting protein-ligand (PL)-binding conformations and strengths, plays key roles in virtual screening (VS). However, the accuracy and speed of current LD methodologies remain suboptimal. Here, we discuss how d...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 25, 2023
Proteins usually perform their cellular functions by interacting with other proteins. Accurate identification of protein-protein interaction sites (PPIs) from sequence is import for designing new drugs and developing novel therapeutics. A lot of comp...
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