Anticancer peptides (ACPs), naturally occurring molecules with remarkable potential to target and kill cancer cells. However, identifying ACPs based solely from their primary amino acid sequences remains a major hurdle in immunoinformatics. In the pa...
Identifying anti-inflammatory peptides (AIPs) and antimicrobial peptides (AMPs) is crucial for the discovery of innovative and effective peptide-based therapies targeting inflammation and microbial infections. However, accurate identification of AIPs...
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...
Protein secondary structure prediction (PSSP) plays a crucial role in resolving protein functions and properties. Significant progress has been made in this field in recent years, and the use of a variety of protein-related features, including amino ...
Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protei...
Journal of the American Society for Mass Spectrometry
39250640
Mass spectrometry (MS) is inherently an information-rich technique. In this era of big data, label-free MS quantification for nontargeted studies has gained increasing popularity, especially for complex systems. One of the cornerstones of successful ...
Journal of chemical information and modeling
39505690
Every year, an estimated 1.5 million people worldwide contract Hepatitis C, a significant contributor to liver problems. Although many studies have explored machine learning's potential to predict antiviral peptides, very few have addressed the probl...
Angewandte Chemie (International ed. in English)
39295564
Designing sequences for specific protein backbones is a key step in creating new functional proteins. Here, we introduce GeoSeqBuilder, a deep learning framework that integrates protein sequence generation with side chain conformation prediction to p...
Journal of the American Society for Mass Spectrometry
39395019
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) data interpretation for organic materials is complicated because of various fragment ions produced from each molecule and the overlapping of certain mass peaks from different molecules. Fragme...
Journal of computational biology : a journal of computational molecular cell biology
39441716
De novo protein sequencing is an important problem in proteomics, playing a crucial role in understanding protein functions, drug discovery, design and evolutionary studies, etc. Top-down and bottom-up tandem mass spectrometry are popular approaches ...