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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 variables, the Entropy Measures of probabilities of occurrence of the amino acids. An intensive study of the Pfam databases is presented with restrictions to families which could be represented by rectangular arrays of amino acids with m rows (protein domains) and n columns (amino acids). This work is also an invitation to scientific research groups worldwide to undertake the statistical analysis with different numbers of rows and columns since we believe in the mathematical characterization of the distribution of amino acids as a fundamental insight on the determination of protein structure and evolution.
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 vary across
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the sequence, define
Background: Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error prone. Man
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the bioc
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in