Briefings in bioinformatics
Nov 22, 2023
The rapid growth of uncharacterized enzymes and their functional diversity urge accurate and trustworthy computational functional annotation tools. However, current state-of-the-art models lack trustworthiness on the prediction of the multilabel clas...
Bioinformatics (Oxford, England)
Oct 3, 2023
MOTIVATION: In recent years, there has been a breakthrough in protein structure prediction, and the AlphaFold2 model of the DeepMind team has improved the accuracy of protein structure prediction to the atomic level. Currently, deep learning-based pr...
Briefings in bioinformatics
Sep 22, 2023
In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has enabled the effi...
Briefings in bioinformatics
Sep 20, 2023
The formation of biomolecular condensates by liquid-liquid phase separation (LLPS) has become a universal mechanism for spatiotemporal coordination of biological activities in cells and has been widely observed to directly regulate the key cellular p...
Briefings in bioinformatics
Sep 20, 2023
The latent features extracted from the multiple sequence alignments (MSAs) of homologous protein families are useful for identifying residue-residue contacts, predicting mutation effects, shaping protein evolution, etc. Over the past three decades, a...
Briefings in bioinformatics
Jul 20, 2023
Computational protein design has been demonstrated to be the most powerful tool in the last few years among protein designing and repacking tasks. In practice, these two tasks are strongly related but often treated separately. Besides, state-of-the-a...
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Jul 1, 2023
Recent advances in Natural Language Processing (NLP) have produced state of the art results on several sequence to sequence (seq2seq) tasks. Enhancements in embedders and their training methodologies have shown significant improvement on downstream t...
Bioinformatics (Oxford, England)
Jun 30, 2023
MOTIVATION: Deep learning-based molecule generation becomes a new paradigm of de novo molecule design since it enables fast and directional exploration in the vast chemical space. However, it is still an open issue to generate molecules, which bind t...
Briefings in bioinformatics
Mar 19, 2023
Great improvement has been brought to protein tertiary structure prediction through deep learning. It is important but very challenging to accurately rank and score decoy structures predicted by different models. CASP14 results show that existing qua...
Bioinformatics (Oxford, England)
Mar 1, 2023
MOTIVATION: Plant Small Secreted Peptides (SSPs) play an important role in plant growth, development, and plant-microbe interactions. Therefore, the identification of SSPs is essential for revealing the functional mechanisms. Over the last few decade...