Related papers: Peptide Classification from Statistical Analysis o…
Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS$^2$) is the major analytical technique in…
Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide…
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
Purpose Nanopore-based molecular sensing and measurement, specifically Deoxyribonucleic acid (DNA) sequencing, is advancing at a fast pace. Some embodiments have matured from coarse particle counters to enabling full human genome assembly.…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
The integration and parallelization of nanopore sensors are essential for improving the throughput of nanopore measurements. Solid-state nanopores traditionally have been used in isolation, which prevents the realization of their full…
Semiconductor nanoplatelets possess exceptional optical properties that make them promising candidates for next-generation optoelectronic applications. However, unlike quantum dots where absorption spectroscopy alone can determine both size…
Rationale: In a shotgun proteomics experiment with data-dependent acquisition, real-time analysis of a precursor scan results in selection of a handful of peaks for subsequent isolation, fragmentation and secondary scanning. This peak…
Protein phosphorylation provides a dynamic readout of cellular signaling yet remains difficult to detect at low abundance and stoichiometry. Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) using particle-in-pore plasmonic…
Solid-state nanopores have received substantial attention in the past years owing to their simplicity and potential applications expected in genomics, sensing, archival information storage, and computing. The underlying sensing technique of…
There are numerous peptides discovered through past decades, which exhibit antimicrobial and anti-cancerous tendencies. Due to these reasons, peptides are supposed to be sound therapeutic candidates. Some peptides can pose low metabolic…
Systematic identification of protein function is a key problem in current biology. Most traditional methods fail to identify functionally equivalent proteins if they lack similar sequences, structural data or extensive manual annotations.…
Post-translational modifications (PTMs) play essential roles in regulating protein structure, function, and cellular signalling. However, peptide level discrimination of hydroxylation at the single-molecule level remains difficult. Here, we…
Purpose: This study aimed to enhance protein sequence classification using natural language processing (NLP) techniques while addressing the impact of sequence similarity on model performance. We compared various machine learning and deep…
We mimic random nanowire networks by the homogeneous, isotropic, and random deposition of conductive zero-width sticks onto an insulating substrate. The number density (the number of objects per unit area of the surface) of these sticks is…
Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…
MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…