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How to characterize short protein sequences to make an effective connection to their functions is an unsolved problem. Here we propose to map the physicochemical properties of each amino acid onto unit spheres so that each protein sequence can be represented quantitatively. We demonstrate the usefulness of this representation by applying it to the prediction of cell penetrating peptides. We show that its combination with traditional composition features yields the best performance across different datasets, among several methods compared. For the convenience of users, a web server has been established for automatic calculations of the proposed features at http://biophy.dzu.edu.cn/SNumD/.
This article was published in the following journal.
The prediction of peptide-protein or protein-protein interactions (PPI) is a challenging task, especially if amino acid sequences are the only information available. Machine learning methods allow us ...
The order of amino acids in a protein sequence enables the protein to acquire a conformation suitable for performing functions, thereby motivating the need to analyse these sequences for predicting fu...
The degree of freedom (DOF) and motion characteristics of a kind of compliant spherical joint were analyzed based on the screw theory, and a new design scheme for force-inversion of the compliant sphe...
Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the...
Protein structure determination has primarily been performed using X-ray crystallography. To overcome the expensive cost, high attrition rate and series of trial-and-error settings, many in-silico met...
The purpose of this study is to evaluate differences in the depth of focus after implantation of a spherical or aspheric IOL in hypermetropic and emmetropic patients. After implantation of...
Purpose:To compare visual performance, total and high order wavefront aberrations (coma, spherical aberration and other terms) and contrast sensitivity in eyes implanted with one monofocal...
The objective of this study is to test and determine whether a high protein diet is efficacious, safe and beneficial to curtail food intake and body weight in obese adult human patients an...
Aim of the present study is to investigate the influence of hyperoxia on the protein expression using the differential analysis of protein expression in tissues (proteomics). In the study,...
The dynamic angio-MR sequences with injection of contrast (CE ARM) allow the study of the vascular anatomy. These sequences, widely used in clinical routine have shown their utility, in pa...
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
A principle of estimation in which the estimates of a set of parameters in a statistical model are those quantities minimizing the sum of squared differences between the observed values of a dependent variable and the values predicted by the model.
A method of chemical analysis based on the detection of characteristic radionuclides following a nuclear bombardment. It is also known as radioactivity analysis. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...