WP4: Case Study. Virtual Laboratory for Protein Structure Prediction. Sara Montagna Modena 30th June, 2008
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1 WP4: Case Study Virtual Laboratory for Protein Structure Prediction Sara Montagna Ingegneria Due Alma Mater Studiorum Università di Bologna a Cesena Modena 30th June, 2008 Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
2 Outline 1 Overview 2 The biological problem The biology of protein folding Protein structure prediction 3 The VLab An AOSE perspective The VLab Requirements 4 A scenario An examples of the system s structure 5 Conclusions Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
3 Overview MEnSA project - Work Package 4 Objective Engineering a case study for investigating and validating the methodologies and infrastructures verifying the effectiveness and usability of the abstractions and tools identified stressing the synergy between the methodological framework and the developed infrastructure Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
4 Overview Virtual Laboratory (VLab) for Protein Structure Prediction Bioinformatics domains of interest proteomic data analysis Towards a Virtual Lab distributed execution of in-silico experiments automatic analysis of data management of large distributed data set distributed cooperation and coordination among heterogeneous actors (biologists, modellers...) The Virtual Lab is a software systems with complex features Agents and MAS for modelling and engineering this complex Virtual Lab Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
5 Outline The biological problem The biology of protein folding 1 Overview 2 The biological problem The biology of protein folding Protein structure prediction 3 The VLab An AOSE perspective The VLab Requirements 4 A scenario An examples of the system s structure 5 Conclusions Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
6 The biological problem The biology of protein folding The Biological Process: Protein Folding Protein folding is the physical process by which a polypeptide folds into its characteristic three-dimensional structure [Wikipedia] Protein structures primary structure secondary structure tertiary structure quaternary structure Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
7 The biological problem The biology of protein folding Amino Acids Are the Subunits of Proteins Basic building blocks of a protein All composed by: carboxyl group (COOH) amino group (H2 N) side chain (R) 20 different types with different side chains along with their chemical properties weak acids, weak bases, hydrophiles, hydrophobes Montagna (Universita di Bologna) WP4: Case Study 30/06/ / 30
8 The Primary Structure The biological problem The biology of protein folding The primary structure is a long chain of amino acids linked together by peptide bonds. This polypeptide constitutes the protein specific primary sequence Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
9 The biological problem The Secondary Structure The biology of protein folding The ordered sequence of amino acids in a protein confer regular conformational forms upon that protein. The secondary structure is the general three-dimensional form of local segments of the protein polypeptidic sequence α-helix β-sheet Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
10 The biological problem The biology of protein folding The Tertiary Structure The tertiary structure refers to the complete three-dimensional structure of the polypeptide units of a given protein. Spatial relationship of different secondary structures to one another within a polypeptide chain How these secondary structures themselves fold into the three-dimensional form of the protein. Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
11 The biological problem The biology of protein folding Summerising: Protein Structure The shape of a protein is specified by its amino acid sequence Protein folds into a conformation of lowest energy The α-helix and the β-sheet are common folding patterns The three dimensional structure represents a conformation with particular chemical properties Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
12 Outline The biological problem Protein structure prediction 1 Overview 2 The biological problem The biology of protein folding Protein structure prediction 3 The VLab An AOSE perspective The VLab Requirements 4 A scenario An examples of the system s structure 5 Conclusions Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
13 The biological problem Protein structure prediction The Importance of the Three-Dimensional Structure The chemical properties are essential for protein function but......the folding mechanism is still not clear the number of possible protein structures is extremely large the physical basis of protein structural stability is not fully understood the experimental determination of the three dimensional structure of a protein is often very difficult and expensive The primary sequence of the protein is often known Protein structure prediction is of high importance. Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
14 The biological problem Protein structure prediction Bioinformatics: Application of Computational Techniques Protein structure prediction methods (manly from AI) Search strategies along the space of possible structures (search strategy and evaluation function) Neural networks for pattern classification Problems The problem size is very high: thousands, millions, billions of possibles structures best the use of metaheuristic (Tabu Search, Simulated Annealing, Evolutionary Computation, Ant Colony Optimization) with the support of physical, chemical or biological informations The evaluation function is extremely difficult to be calculated accurately use of highly simplified models of biological phenomena Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
15 The VLab The VLab System that can support biologists and bioinformatics in the problem of protein structure prediction. sharing the data integration of multiple users and algorithms efforts interactive and cooperative work Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
16 Outline The VLab An AOSE perspective 1 Overview 2 The biological problem The biology of protein folding Protein structure prediction 3 The VLab An AOSE perspective The VLab Requirements 4 A scenario An examples of the system s structure 5 Conclusions Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
17 The VLab An AOSE perspective Why this Case Study for MEnSA Project The system is massively knowledge-based, as it requires the definition of specific and rigorous ontologies The system requires the management of multiple processes and tasks for the elaboration of the knowledge and data at different levels: integrating heterogeneous skills and methods enabling the interaction with human users who are involved in the processes as external observers, controllers and analysts. Works on this line [Addis et al., 2007] [Bortolussi et al., 2007] Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
18 Outline The VLab The VLab Requirements 1 Overview 2 The biological problem The biology of protein folding Protein structure prediction 3 The VLab An AOSE perspective The VLab Requirements 4 A scenario An examples of the system s structure 5 Conclusions Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
19 The VLab The VLab Requirements First Requirement Hybrid or parallel algorithms have improved search patterns obtaining reasonably good approximate solutions [Milano and Roli, 2004]. Implementation of methods to Define the models and strategies (search strategies, neural net...) parameters and tuned them through a learning process Integrate models and algorithms Define the problem s model a set of variables, X = [x 1,..., x n ] variable domains, D i i = 1,..., n constraints among variables an evaluation function Elaborate the knowledge Produce a possible candidate solution Identify new information on the protein structure Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
20 Second Requirement The VLab The VLab Requirements Organization and representation of data and knowledge Shared data structure where informations are accessible by all the users are organized in hierarchical levels At each level data contain more and more informations data are partial solutions to the problem Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
21 Third Requirement The VLab The VLab Requirements Human users interaction Interface the VLab with biologists, bioinfomatics for adding knowledge on the protein s properties giving feedbacks on the partial solutions collected selecting the algorithms designing models and search strategies Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
22 The VLab The VLab Requirements Fourth Requirement Internet resources exploitation Acquire knowledge and data spread among different Internet sources Filter and organise them on the shared data structure Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
23 The VLab The VLab Requirements How the Overall System Looks Like A set of independent modules, named knowledge sources, which contain specific knowledge about a problem domain. A shared data structure through which the knowledge sources communicate to each other. A set of algorithms and models for the elaboration of the knowledge. A set of functionality for allowing the activity of human users (the experts). A control mechanism which determines the order in which the knowledge sources will operate on the data. Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
24 Outline A scenario An examples of the system s structure 1 Overview 2 The biological problem The biology of protein folding Protein structure prediction 3 The VLab An AOSE perspective The VLab Requirements 4 A scenario An examples of the system s structure 5 Conclusions Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
25 A scenario Shared Data Structure Organisation An examples of the system s structure At each level incorporation of biological knowledge, solutions provided by algorithms, feedbacks from experts on first knowledge on the primary sequence of the protein second hydrofobic-hydrophilic (HP) model third n random protein conformations on 2D or 3D lattice fourth small set of plausible protein conformations fifth the optimal protein conformation Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
26 How the VLab Looks Like A scenario An examples of the system s structure Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
27 A scenario An examples of the system s structure Metaheuristic for Protein Folding Prediction Genetic algorithms Exploration of the molecular energy surface Optimization of the energy function E Identification of the best set of parameters population size mutation recombination local search operators Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
28 Conclusions Conclusions Already done The biological problems and the necessity of a VLab The Vlab s requirements To do Refining the system s requirements according to your feedbacks Representing the case study with the different methodologies... Doing the same job with the new meta-model and methodology Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
29 Bibliography Conclusions Addis, A., Armano, G., Mascia, F., and Vargiu, E. (2007). Protein secondary structure prediction through a cooperative multiagent learning approach. System and Information Sciences Notes, 2(1): Bortolussi, L., Dovier, A., and Fogolari, F. (2007). Agent-based protein structure prediction. Journal of Multi Agents and Grid Systems, 3(2). Milano, M. and Roli, A. (2004). Magma: a multiagent architecture for metaheuristics. IEEE Transactions on Systems, Man, and Cybernetics, Part B, 34(2): Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
30 Conclusions WP4: Case Study Virtual Laboratory for Protein Structure Prediction Sara Montagna Ingegneria Due Alma Mater Studiorum Università di Bologna a Cesena Modena 30th June, 2008 Montagna (Università di Bologna) WP4: Case Study 30/06/ / 30
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