Functional proteomics modeling system

Abstract

The invention develops models of functional proteomics. Simulation scenarios of protein pathway vectors and protein-protein interactions are modeled from limited information in protein databases. The system focuses on three integrated subsystems, including (1) a system to model protein-protein interactions using an evolvable Global Proteomic Model (GPM) of functional proteomics to ascertain healthy pathway operations, (2) a system to identify haplotypes customized for specific pathology using dysfunctional protein pathway simulations of the function of combinations of single nucleotide polymorphisms (SNPs) so as to ascertain pathology mutation sources and (3) a pharmacoproteomic modeling system to develop, test and refine proposed drug solutions based on the molecular structure and topology of mutant protein(s) in order to manage individual pathologies. The system focuses on simulating the degenerative genetic disease categories of cancer, neurodegenerative diseases, immunodegenerative diseases and aging. The system reveals approaches to reverse engineer and test personalized medicines based upon dysfunctional proteomic pathology simulations.

1 . A bioinformatics system for functional proteomics modelling, the system comprising one, two or all three of the following: 
 a first subsystem which involves development of an evolvable Global Proteomics Model, which uses data from the Human Genome Project and from protein and genetic databases on structural proteomics and which supplies a foundation for simulations of healthy protein-protein interactions;    a second subsystem which involves development of simulations to identify the operation and source of individual diseases in dysfunctional protein-protein interactions; and    a third subsystem which involves development of simulations for pharmacoproteomics in which prospective drug targets are modelled, tested and refined for optimum effectiveness for individualized therapy.    
   
   
       2 . A bioinformatics system as claimed in  claim 1 , in which the system employs intelligent mobile software agents (IMSAs) which operate in a multi-agent system (MAS) in order to carry out computational operations.  
   
   
       3 . A bioinformatics system as claimed in  claim 1 , in which the IMSAs work together to process parts of complex computations in order to solve complex FP optimization problems.  
   
   
       4 . A bioinformatics system as claimed in  claim 1 , in which the simulations generated by IMSAs in the three main categories of FP modelling, dysfunctional proteomic modelling and pharmacoproteomics modelling, thereby allowing the emulation and reconstruction of complex self-organizing biological systems.  
   
   
       5 . A bioinformatics system as claimed in  claim 1 , in which the GPM uses data from genetic and structural proteomic databases to develop a functional proteomic model for understanding general protein-protein interactions.  
   
   
       6 . A bioinformatics system as claimed in  claim 1 , in which, in the second sub-system, IMSAs generate simulations from data sets involving dysfunctional protein interactions.  
   
   
       7 . A bioinformatics system as claimed in  claim 1 , in which the third subsystem is arranged, once a disease is analyzed via proteomic simulations, to analyse the mutant proteins' structures  
   
   
       8 . A bioinformatics system as claimed in  claim 1 , in which the active computational system is arranged to design a compound to solve the problem with each distinctive mutant protein.  
   
   
       9 . A bioinformatics system as claimed in  claim 1 , in which the GPM and other database information sources generate simulations that emulate molecular protein interactions, and optionally the simulations have multiple vectors and scenarios.  
   
   
       10 . A bioinformatics system as claimed in  claim 1 , in which the IMSAs use the GPM as a source of comparison to assemble information about dysfunctional protein behaviour.  
   
   
       11 . An adaptive dynamic computer system for modelling functional proteomics having a plurality of system layers interconnected to one another, comprising: 
 a first layer including human genome databases;    a second layer including structural proteomic libraries;    a third layer including a global proteomic model;    a fourth layer including functional proteomic maps;    a fifth layer including modelling of protein behaviours;    a sixth layer including a multi agent system of intelligent mobile software agents;    a seventh layer including simulations of protein interactions;    an eighth layer including individual pathology identification of mutation combinations;    a ninth layer including pharmacoproteomics;    a tenth layer including a pathology applications category typology;    an eleventh layer including oncoproteomics, neuroproteomics, immunoproteomics and gerontoproteomics.