Welcome to this bioinformatics lab on data manipulation using online and server tools.As the theme, we have chosen to study of the interaction between Frataxin and pancreatic cancer.
Th is is the lab template: The context is a biological context based on a real biological problem. And a given hypothesisI don’t use computer science, strong word.When you read this template, you have a different view than an informatician.You want to understand the process to build the used tools.The architecture of the systemThe algorithm implementationThe quality of the resulting dataAnd so on
Session ii g2 lab modeling mmc
Systems Biology and ProteinHomology ModelingTheme: MRSA Acetate Kinase and MetabolicNetwork ModelingLab #2Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013Etienne.email@example.com
Context0. Specification & AimsLab #2Statement of problem / Case study:MRSA Acetate Kinase ( SAV 1711 from MRSA Mu50 strain) was found in our preliminary study on Silico. It is essential to bacteria growth and absent in humans. Currently, thereis no FDA approved antibiotics targeting bacterial central metabolism, these bacterial sites have not yet been exposed to antibacterial agents and therefore will be less likely todevelop a drug resistance.ModelingKeywords:Bio: MRSA, Acetate KinaseInformatics: programing, bioinformatics tools, gettingand exporting data. Validating models.16 Korean Bioinformation Center, 2010Reduced expression of frataxin is thecause of Friedrichs ataxia (FRDA), alethal neurodegenerative disease, howabout liver cancer?Aim: The purpose of this lab is to understandhow Protein, Chemical, and MetabolicNetwork Modeling can be used for researchtopics. This process will allow researchersmore information to have more informationavailable.Acquired skillsOnline and server tools:- Protein Homology Modeling- Model Evaluation on ERRAT- Chemical Modeling through OCHEM server- Metabolic Network Modeling using BioModels and VirtualCell.Biological Hypothesis2Resolution ProcessT2. Chemical ModelingObjective: Use of OCHEM and PubChem to extract information about the desired chemical models.T3. Metabolic Network ModelingObjective: Use of BioModels and Virtual Cell to extract data about MetabolicNetworking.T2.1. Using OCHEM and PubChemT3.1. Finding a model using BioModelsT3.2. Validating the ModelT3.3. Virtual CellT1. Protein Homology Modeling (PMP)Objective: Use of PMP website to evaluate different protein models via the ERRATwebsite.T1.1 Template SelectionT1.2. Model Evaluation on ERRAT
Protein Modeling Systems Biology and Protein ModelingT1. Protein ModelingObjective: Use of PMP website to evaluate different protein models via the ERRAT website.T1.1. Template SelectionOn the Protein Modeling Portal website: http://www.proteinmodelportal.org1) Click on “interactive modeling” and put in your Name and E-Mail address (results will be sent to your e-mail)2) Copy and paste the amino acid sequence from the word document “Amino Acid Sequence”3) Check all six boxes below (the different Databases used) Be sure to select the first option under ModWeb andthe check the box under M4T.4) Submit Query5) Once execution has gone through, select the different Database results. Because this query takes a long time wehave the finished results available.6) Open jmol, then go to “File”, “Open” and open the file in your student folder called “Swiss Model Result” (a pdbfile)Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013T1.2. Model Evaluation on ERRATWill have many models, in order to select best fitting model we use model evaluation tools such as ERRAT.On ERRAT website: http://nihserver.mbi.ucla.edu/ERRATv2/1) Click “browse” (or “choose file”) and select the PDB file “Swiss Model Result.pdb” in your folder and click“send file”2) The results will open and you can look at the information provided such as the quality of the model chosen.3) Open the PDF version by clicking on “PDF file here” and save.4) You can do this with all of the models you receive in your e-mail and compare the quality of each in order tochose the best model
Chemical ModelingT2. Chemical ModelingObjective: Use of OCHEM and PuubChem to extract information about the desired chemicalmodels.T2.1. Using OCHEM and PubChemOn the OCHEM website: http://www.ochem.eu/home/show.doo Click on “Run predictions” and “login as guest”. Accept the “Terms and Agreements” formo Then select all the boxes under the “What would you like to predict?”o Then open a new tab and go to the PubChem website: http://pubchem.ncbi.nlm.nih.gov/o Search under the “Compound” tab for “protein kinase” and select the “protein kinase inhibitor M (6-24)”o Scroll down and copy the sequence from “canonical SMILES” and paste to the “Provide Name/CAS-RN/SMILES” on OCHEM websiteo Select the “Provide Name/CAS-RN/SMILES” and click “Run predictions”o Once results show up you can read and deduce the information provided.Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013Systems Biology and Protein Modeling
Metabolic Network ModelingT3. Metabolic Network ModelingObjective: Use of BioModels and Virtual Cell to extract data about Metabolic Networking.T3.1. Finding a model using BioModelsOn the BioModels website: http://www.ebi.ac.uk/biomodels-main/o Search “acetate kinase” select the 3rd, “Cell Cycle 6var”o Place your mouse over “Download SBML” in the top left of the screen, and select “SMBL L2 V4 (curated)” andsave the file. This file will already be in your Student Folder as “AcetateKinaseModel.xml”Etienne Z. GnimpiebaBRIN WS 2013Mount Marty College – June 24th 2013T3.2. Validating the ModelOn the SMBL Validator website: http://sbml.org/validator/o Click “Browse” and open the “AcetateKinaseModel.xml”o Click “Validate Now” and check its validitySystems Biology and Protein ModelingT3.3. Virtual Cello Go to your Student Folder in “Tools” and run “vcell”. Exit the boxes that pop upo Click on “Reactions” tab and double click “add new here” in the centero On the left side of the arrow put an “S” (for substrate) and on the right side put a “P” (for product) [S -> P]o Push enter to create your reactiono Make sure you are still on the new reaction and pull down “Kinetic Type” at the bottom and select “Henri-Michaelis-Menten (Irreversible)..”o Edit the “Expression” for “Km” to be “0.01” as well as the “Vmax” to be “10.0” by double clicking under “Expression”o Click on the “Applications” on the left, pull down “Add New” in the middle and select “Deterministic”o Click on “Application: Application0”o Click “New Simulation” [ ] then click “Edit” [ ]o A window will pop up, adjust value under “Default” by clicking the box under “Scan” for; “P_init_uM” to min “0.1”and max “100”; “S_init_uM” to min “0.1” max “100”o Click “ok”o Push the play button [ ] in the upper right corner to simulate the modelo The results will pop up in a new window. You can choose which results you see by selecting them on the left