Protein science : a publication of the Protein Society
Dec 1, 2022
Atomic interactions play essential roles in protein folding, structure stabilization, and function performance. Recent advances in deep learning-based methods have achieved impressive success not only in protein structure prediction, but also in prot...
Bioinformatics (Oxford, England)
Nov 30, 2022
MOTIVATION: The advent of massive DNA sequencing technologies is producing a huge number of human single-nucleotide polymorphisms occurring in protein-coding regions and possibly changing their sequences. Discriminating harmful protein variations fro...
Briefings in bioinformatics
Sep 20, 2022
A newly invented post-translational modification (PTM), phosphoglycerylation, has shown its essential role in the construction and functional properties of proteins and dangerous human diseases. Hence, it is very urgent to know about the molecular me...
Bioinformatics (Oxford, England)
Sep 16, 2022
SUMMARY: Recently, deep learning models, initially developed in the field of natural language processing (NLP), were applied successfully to analyze protein sequences. A major drawback of these models is their size in terms of the number of parameter...
Structure (London, England : 1993)
Aug 4, 2022
Accurate protein structure predictors use clusters of homologues, which disregard sequence specific effects. In this issue of Structure, Weißenow and colleagues report a deep learning-based tool, EMBER2, that efficiently predicts the distances in a p...
Nucleic acids research
Jul 5, 2022
Recent advances in machine learning and natural language processing have made it possible to profoundly advance our ability to accurately predict protein structures and their functions. While such improvements are significantly impacting the fields o...
Protein science : a publication of the Protein Society
Jul 1, 2022
Using the molecular modeling program Rosetta, we designed a de novo protein, called SEWN0.1, which binds the heterotrimeric G protein Gα The design is helical, well-folded, and primarily monomeric in solution at a concentration of 10 μM. However, whe...
Bioinformatics (Oxford, England)
Jun 27, 2022
SUMMARY: Identifying the protein-peptide binding residues is fundamentally important to understand the mechanisms of protein functions and explore drug discovery. Although several computational methods have been developed, most of them highly rely on...
Bioinformatics (Oxford, England)
May 26, 2022
MOTIVATION: A high-quality sequence alignment (SA) is the most important input feature for accurate protein structure prediction. For a protein sequence, there are many methods to generate a SA. However, when given a choice of more than one SA for a ...
Briefings in bioinformatics
May 13, 2022
In the last few decades, antimicrobial peptides (AMPs) have been explored as an alternative to classical antibiotics, which in turn motivated the development of machine learning models to predict antimicrobial activities in peptides. The first genera...