The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but the short lengths of AMPs pose a challenge for computational prediction. Here we combined multiple natural language processing neural network models, including LST...
OpenSWATH is an analysis toolkit commonly used for data independent acquisition (DIA). Although the output of OpenSWATH is controlled at 1% false discovery rate (FDR), the output report still contains many peptide precursors with low similarity fragm...
Cancer is one of the most dangerous threats to human health. One of the issues is drug resistance action, which leads to side effects after drug treatment. Numerous therapies have endeavored to relieve the drug resistance action. Recently, anticancer...
Journal of chemical information and modeling
Feb 7, 2022
Nowadays, machine learning and deep learning approaches are widely utilized for generative chemistry and computer-aided drug design and discovery such as de novo peptide and protein design, where target-specific peptide-based/protein-based therapeuti...
International journal of molecular sciences
Feb 3, 2022
As one of the most important post-translational modifications (PTMs), phosphorylation refers to the binding of a phosphate group with amino acid residues like Ser (S), Thr (T) and Tyr (Y) thus resulting in diverse functions at the molecular level. Ab...
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2022
Evolution of drug-resistant microbial species is one of the major challenges to global health. Development of new antimicrobial treatments such as antimicrobial peptides needs to be accelerated to combat this threat. However, the discovery of novel a...
Machine learning with multi-layered artificial neural networks, also known as "deep learning," is effective for making biological predictions. However, model interpretation is challenging, especially for sequential input data used with recurrent neur...
Recently, deep learning techniques have been developed for various bioactive peptide prediction tasks. However, there are only conventional machine learning-based methods for the prediction of anti-angiogenic peptides (AAP), which play an important r...
Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry an...
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we show that, although these deep learning approaches have originally been develop...