Related papers: Peptide Classification from Statistical Analysis o…
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…
We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…
Nanobodies are small antibody fragments derived from camelids that selectively bind to antigens. These proteins have marked physicochemical properties that support advanced therapeutics, including treatments for SARS-CoV-2. To realize their…
Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a…
We present a tight-binding model study of a two-terminal graphene nanopore device for sequential determination of DNA bases. Using Green's function technique we investigate the changes in electronic transport properties of the device due to…
Digital assays represent a shift from traditional diagnostics and enable the precise detection of low-abundance analytes, critical for early disease diagnosis and personalized medicine, through discrete counting of biomolecular reporters.…
Mass spectrometry provides a high-throughput approach to identify proteins in biological samples. A key step in the analysis of mass spectrometry data is to identify the peptide sequence that, most probably, gave rise to each observed…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as…
In this work, we propose a novel centrality metric, referred to as star centrality, which incorporates information from the closed neighborhood of a node, rather than solely from the node itself, when calculating its topological importance.…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
Elucidating exocytosis processes provide insights into cellular neurotransmission mechanisms, and may have potential in neurodegenerative diseases research. Amperometry is an established electrochemical method for the detection of…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein…
Peptide sequencing-the process of identifying amino acid sequences from mass spectrometry data-is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional…
{\it De novo} protein sequencing is essential for understanding cellular processes that govern the function of living organisms and all post-translational events and other sequence modifications that occur after a protein has been…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
We illustrate the use of tools (asymptotic theories of standard error quantification using appropriate statistical models, bootstrapping, model comparison techniques) in addition to sensitivity that may be employed to determine the…
In recent era prediction of enzyme class from an unknown protein is one of the challenging tasks in bioinformatics. Day to day the number of proteins is increases as result the prediction of enzyme class gives a new opportunity to…
Temporary changes in electrical resistance of a nanopore sensor caused by translocating target analytes are recorded as a sequence of pulses on current traces. Prevalent algorithms for feature extraction in pulse-like signals lack…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…