Related papers: Sequencing proteins with transverse ionic transpor…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
The ability to characterize proteins at sequence-level resolution is vital to biological research. Currently, the leading method for protein sequencing is by liquid chromatography mass spectrometry (LC-MS) whereas proteins are reduced to…
The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged prefix and suffix subsequences, and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to…
Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
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…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We review recent advances in the DNA sequencing based on the measurement of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major…
Peptide de novo sequencing is a method used to reconstruct amino acid sequences from tandem mass spectrometry data without relying on existing protein sequence databases. Traditional deep learning approaches, such as Casanovo, mainly…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
We suggest to discriminate single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…