相关论文: The Protein Family Classification in Protein Datab…
A pattern Recognition of a probability distribution of amino acids is obtained for selected families of proteins. The mathematical model is derived from a theory of protein families formation which is derived from application of a Pauli's…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
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 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…
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…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
In this paper, we address the problem of identifying protein functionality using the information contained in its aminoacid sequence. We propose a method to define sequence similarity relationships that can be used as input for…
Efficient automatic protein classification is of central importance in genomic annotation. As an independent way to check the reliability of the classification, we propose a statistical approach to test if two sets of protein domain…
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…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
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…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of…
Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM…