Journal of bioscience and bioengineering
Jul 10, 2025
The construction of small proteins by removing amino acid subsequences that are not involved in function, activity, or structure is crucial for bioprocessing and drug development. Traditional design methods often focus on reconstructing functional mo...
Natural topological proteins exhibit unique properties including enhanced stability, controlled quaternary structures, and dynamic switching properties, highlighting topology as a unique dimension in protein engineering. Although artificial design an...
Peptide-level quantification using mass spectrometry (MS) is no trivial task as the physicochemical properties affect both response and detectability. The specific amino acid (AA) sequence affects these properties, however the connection between sequ...
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topolog...
INTRODUCTION: Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation induced deaminase (AID) is essential for robust, long-term humoral immunity against pathogen and vaccine antigens. AID mutates cytosines preferentially wit...
Journal of computational biology : a journal of computational molecular cell biology
Jan 21, 2022
Template-based modeling (TBM), including homology modeling and protein threading, is one of the most reliable techniques for protein structure prediction. It predicts protein structure by building an alignment between the query sequence under predict...
Protein kinase-inhibitor interactions are key to the phosphorylation of proteins involved in cell proliferation, differentiation, and apoptosis, which shows the importance of binding mechanism research and kinase inhibitor design. In this study, a no...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
RNA-binding proteins (RBPs) have a significant role in various regulatory tasks. However, the mechanism by which RBPs identify the subsequence target RNAs is still not clear. In recent years, several machine and deep learning-based computational mode...
Accurate prediction of neoantigens and the subsequent elicited protective anti-tumor response are particularly important for the development of cancer vaccine and adoptive T-cell therapy. However, current algorithms for predicting neoantigens are lim...
DNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification responsible for many biological functions. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money...
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