Amino acid scales are crucial for protein prediction tasks, many of them being curated in the AAindex database. Despite various clustering attempts to organize them and to better understand their relationships, these approaches lack the fine-grained ...
Anticancer peptides (ACPs) perform a promising role in discovering anti-cancer drugs. The growing research on ACPs as therapeutic agent is increasing due to its minimal side effects. However, identifying novel ACPs using wet-lab experiments are gener...
Predicting protein function from protein sequence, structure, interaction, and other relevant information is important for generating hypotheses for biological experiments and studying biological systems, and therefore has been a major challenge in p...
The recognition of DNA-binding proteins (DBPs) is the crucial step to understanding their roles in various biological processes such as genetic regulation, gene expression, cell cycle control, DNA repair, and replication within cells. However, conven...
In recent years, there has been a notable increase in the scientific community's interest in rational protein design. The prospect of designing an amino acid sequence that can reliably fold into a desired three-dimensional structure and exhibit the i...
The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous methods and...
Statistical applications in genetics and molecular biology
Jul 1, 2024
Understanding a protein's function based solely on its amino acid sequence is a crucial but intricate task in bioinformatics. Traditionally, this challenge has proven difficult. However, recent years have witnessed the rise of deep learning as a powe...
Asparagine peptide lyase (APL) is among the seven groups of proteases, also known as proteolytic enzymes, which are classified according to their catalytic residue. APLs are synthesized as precursors or propeptides that undergo self-cleavage through ...
Acta crystallographica. Section D, Structural biology
Jun 27, 2024
When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification...
As of now, more than 60 years have passed since the first determination of protein structures through crystallography, and a significant portion of protein structures can be predicted by computers. This is due to the groundbreaking enhancement in pro...