Journal of chemical theory and computation
Mar 24, 2023
Finding new enzyme variants with the desired substrate scope requires screening through a large number of potential variants. In a typical enzyme engineering workflow, it is possible to scan a few thousands of variants, and gather several candidates...
Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large langu...
Signal transduction and targeted therapy
Mar 14, 2023
AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most chal...
Cell-penetrating peptides (CPPs) have great potential to deliver bioactive agents into cells. Although there have been many recent advances in CPP-related research, it is still important to develop more efficient CPPs. The development of CPPs by in s...
Journal of bioinformatics and computational biology
Mar 9, 2023
Protein secondary structure prediction (PSSP) is an important and challenging task in protein bioinformatics. Protein secondary structures (SSs) are categorized in regular and irregular structure classes. Regular SSs, representing nearly 50% of amino...
The inverse protein folding problem, also known as protein sequence design, seeks to predict an amino acid sequence that folds into a specific structure and performs a specific function. Recent advancements in machine learning techniques have been su...
Predicting the function of a protein from its amino acid sequence is a long-standing challenge in bioinformatics. Traditional approaches use sequence alignment to compare a query sequence either to thousands of models of protein families or to large ...
Protein-Protein Interactions (PPIs) are fundamental means of functions and signalings in biological systems. The massive growth in demand and cost associated with experimental PPI studies calls for computational tools for automated prediction and und...
Journal of the mechanical behavior of biomedical materials
Feb 22, 2023
The silk fiber is increasingly being sought for its superior mechanical properties, biocompatibility, and eco-friendliness, making it promising as a base material for various applications. One of the characteristics of protein fibers, such as silk, i...
Current opinion in structural biology
Feb 18, 2023
The function of proteins can often be inferred from their three-dimensional structures. Experimental structural biologists spent decades studying these structures, but the accelerated pace of protein sequencing continuously increases the gaps between...