Related papers: Filovirus Glycoprotein Sequence, Structure and Vir…
This study introduces the Supervised Magnitude-Altitude Scoring (SMAS) methodology, a machine learning-based approach, for analyzing gene expression data obtained from nonhuman primates (NHPs) infected with Ebola virus (EBOV). We utilize a…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
I use a mean-field approximation to show the rapid collapse of heteropolymers from random walk size to a much smaller, molten globule state due to hydrophobic interactions, to be followed by a slower annealing process in which there is…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
A differential equations model is developed for the 2014 Ebola epidemics in Sierra Leone, Liberia, and Guinea. The model describes the dynamic interactions of the susceptible and infected populations of these countries. The model…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other…
The reason of significantly higher transmissibility of SARS Covid (2019 CoV-2) compared to SARS Covid (2003 CoV) and MERS Covid (2012 MERS) can be attributed to mutations reported in structural proteins, and the role played by…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…