Related papers: Peptide Classification from Statistical Analysis o…
The gesture recognition using motion capture data and depth sensors has recently drawn more attention in vision recognition. Currently most systems only classify dataset with a couple of dozens different actions. Moreover, feature…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…
Graph classification aims to categorize graphs based on their structural and attribute features, with applications in diverse fields such as social network analysis and bioinformatics. Among the methods proposed to solve this task, those…
Biological matrices are rich in information related to life processes, serving as invaluable media for assessing an individual's overall physiological status and its dynamic fluctuations, as well as crucial foundations for disease…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
Anticancer peptides (ACPs) are a group of peptides that exhibite antineoplastic properties. The utilization of ACPs in cancer prevention can present a viable substitute for conventional cancer therapeutics, as they possess a higher degree…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
Advanced nanopore measurements allow structural probing of molecules with high spatial and temporal resolution. We report high signal-to-noise, 1-10 MHz bandwidth, translocation measurements of the multi-state folding of heme protein…
Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Herein, we present DeepRT, a deep learning based software for peptide retention time prediction.…
Image segmentation for video analysis plays an essential role in different research fields such as smart city, healthcare, computer vision and geoscience, and remote sensing applications. In this regard, a significant effort has been…
Spiking neural networks (SNN) hold the promise of being a more biologically plausible, low-energy alternative to conventional artificial neural networks. Their time-variant nature makes them particularly suitable for processing…
Capturing the dynamical properties of time series concisely as interpretable feature vectors can enable efficient clustering and classification for time-series applications across science and industry. Selecting an appropriate feature-based…
In this study, we examine the mechanism of nanopore-based DNA sequencing using a voltage bias across a graphene nanoribbon. Using density functional theory and a non-equilibrium Green's function approach, we determine the transmission…
We present a comprehensive approach to the modeling, performance analysis, and design of clustered molecular nanonetworks in which nano-machines of different clusters release an appropriate number of molecules to transmit their sensed…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
The knowledge regarding the function of proteins is necessary as it gives a clear picture of biological processes. Nevertheless, there are many protein sequences found and added to the databases but lacks functional annotation. The…