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...
Bioinformatics (Oxford, England)
Apr 28, 2022
MOTIVATION: Drug discovery has witnessed intensive exploration of predictive modeling of drug-target physical interactions over two decades. However, a critical knowledge gap needs to be filled for correlating drug-target interactions with clinical o...
Bioinformatics (Oxford, England)
Apr 12, 2022
MOTIVATION: The interactions between proteins and other molecules are essential to many biological and cellular processes. Experimental identification of interface residues is a time-consuming, costly and challenging task, while protein sequence data...
Bioinformatics (Oxford, England)
Apr 12, 2022
SUMMARY: Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for t...
Briefings in bioinformatics
Mar 10, 2022
Protein secretion has a pivotal role in many biological processes and is particularly important for intercellular communication, from the cytoplasm to the host or external environment. Gram-positive bacteria can secrete proteins through multiple secr...