Methods, systems, algorithyms and means for describing the possible conformations of actual and theoretical proteins and for evaluating actual and theoretical proteins with respect to folding, overall

Abstract

Methods, systems, algorithms and means for describing, analyzing and predicting protein folding motifs and other structures are provided. In one aspect, the Protein Folding Shape Code (PFSC) methods,systems, algorithms and means of the present invention apply generally to all of the categories of protein analysis and description, and are especially relevant to the geometric analyses and descriptions of proteins from their respective sequences or sequence portions. In a novel approach, the present inventions render analyses with respect to the alpha carbons of five-amino acid elements of a protein, utilizing available data to derive torsion angles and pitch distances, to thereby generate a series of overlapping analyses that can be expressed by a plurality of 27 vectors. Methods, systems and algorithms of the invention can be embodied in any computing device or portion thereof, and are adaptable to describe, analyze and predict the folding and other three-dimensional aspects of the structures of biomolecules such as nucleic acids, carbohydrates and glycoproteins. As yet another advantage, the present invention is adaptable as a tool for describing the conformations of many other organic molecules, and are thus especially suitable for use in the design of drugs, and the discovery and design of molecules which are to be adapted to interact with drugs.

Description

[0001] Pre-declaration [0002] Before the application of this patent to the World Patent Cooperation Treaty (PCT), the provisional application 60 / 898,529 of the US patent was filed on January 31, 2007, and the US patent application was filed on November 23, 2007. Patent Provisional Application 61 / 004,094, and US Patent Provisional Application 61 / 062,775 filed January 29, 2008. technical field [0003] The present invention relates to biotechnology, in particular to methods, systems and devices for describing the conformation of proteins and evaluating them in terms of folding, overall shape and structural sequence. Background technique [0004] Although the three-dimensional structure of proteins can be obtained at the atomic level through crystal structure X-ray diffraction, nuclear magnetic resonance spectroscopy or computer simulation methods, describing the folded shape of proteins is still a challenging topic. In the protein fold structure, the configuration of some f...

AI Technical Summary

Problems solved by technology

[0015] In summary, these traditional methods are still unable to satisfactorily describe protein folding and conformation

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