Related papers: Minimal Immunogenic Epitopes Have Nine Amino Acids
Thermodynamic profiles, based on bioinformatic hydropathicity scales and membrane-fitted sliding windows, exhibit accurately level sets of hydrophobic peaks or valleys in the constant fragment Fc of monoclonal antibodies. These sets provide…
Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods…
What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
This paper reports about an approach to the classification of proteins' primary structures taking advantage of the Self Organizing Maps algorithm and of a numerical coding of the aminoacids based upon their physico-chemical properties.…
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells are largely based on transcriptomic single-cell…
In-vivo toxicological studies are characterized by multiple primary endpoints with quite different scales. Whereas guidelines and publications provide various statistical tests for normally distributed endpoints (such as organ weights) and…
In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…
The most cost-effective blood-based, noninvasive molecular cancer biomarkers are based on p53 epitopes and MUC1 tandem repeats. Here we use dimensionally compressed bioinformatic fractal scaling analysis to compare the two distinct and…
Identification of antimicrobial peptides is an important and necessary issue in today's era. Antimicrobial peptides are essential as an alternative to antibiotics for biomedical applications and many other practical applications. These…
The durability of facades is heavily affected by multiple factors like microbial growth and weather conditions among others. Biocides are often used to resist these factors and protect the facades. However, the biocides get washed out due…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Identifying the targets of an antimicrobial peptide is a fundamental step in studying the innate immune response and combating antibiotic resistance, and more broadly, precision medicine and public health. There have been extensive studies…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
Approximate Bayesian Computation is widely used to infer the parameters of discrete-state continuous-time Markov networks. In this work, we focus on models that are governed by the Chemical Master Equation (the CME). Whilst originally…
Biomarker is a critically important tool in modern clinical diagnosis, prognosis, and classification/prediction. However, there are fiscal and analytical barriers to biomarker research. Selective Genotyping is an approach to increasing…
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein--ligand interaction energies, enzymatic reaction energies, or spectroscopic…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…