Introduction to Computational Biology: Curriculum Development

Ruijun ZhaoKai ShenShaneka SimmonsPresented by: 1Creating the Curriculum for computational Biology1 QUESTIONS CONSIDERED FOR EFFECTIVE COURSE DESIGN What students will you target and what are their needs?What do you want them to learn?What content matter will engage the students?What will your students discover about the class that they can relate to everyday life?Drug designEnzyme modification Food IndustryWhat are your strengths put into this course?Teach students how to identify and solve problems?Teach students how to utilize modern tools and promote current topics of interest?Who will be your collaborators (invited speakers, course development)

3 3Course ObjectivesBrainstorm

4Shaneka Simmons, Jackson State University Introduction to Data Visualization

Kai Shen, Savannah State University Introduction to Computational Biochemistry

Ruijun Zhao, Minnesota State University Introduction to Molecular Dynamics

Course Collaboration

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Curriculum 4

6Course ObjectivesStudents will be able to set up, run a simulation and interpret the simulation results through case studies. Students will be able to utilize mainstream bioinformatics tools.Students learn to effectively collaborate with their peers.Student Preliminary AssessmentFoldit game at the introduction of the class and after the introduction to molecular dynamicsHomework assignments Concept understanding Justification of protein selectionGroup projectsExploring tools and solve a real problemWhat is the structure-function relationship Proteopedia (www.proteopedia.org)Math Scoring using Protein DockingFuture WorkDesign modules Video modules Powerpoint presentationsSource files for community utilizationIntroductory teaching tutorials for studentsDesign online courses

Why should we care? Conveying: Introduction to Computational Biology

http://www.ebi.ac.uk/luscombe/docs/imia_review.pdf10 5Sample course topics 11Module 1: Protein Structures-Basic Introduction Chemical bonds, weak forces involved in protein structuresAmino acids, primary structures, secondary, and tertiary structuresSide chains of protein residues, protein-protein/protein-ligand interaction

Module 2. Molecular VisualizationVisualization softwareDescriptionURLPDBeEBI's Protein Data Bank in Europehttp://www.ebi.ac.uk/pdbe/PDBRCSBs database of protein http://www.pdb.org/PyMOLMolecular visulization softwarehttp://www.pymol.orgJMolOpen source Java Viewer for 3D structureshttp://jmol.sourceforge.netVMDMolecular visualization and dynamics software www.ks.uiuc.edu/Research/vmd/

Module 3. Protein DockingPrinciples of DockingReview interactions, chemical bonds, and protein structuresSearch algorithmScoring functionsWorking with docking software suits with a focus on open source packagesHADDOCK, AUTODOCK, ZDOCK, etc.ApplicationDrug discovery Tutorial http://ringo.ams.sunysb.edu/index.php/2012_DOCK_tutorial_with_Streptavidin

Docking Software Packages

Module 4: Molecular Dynamics

Selected Textbooks for Molecular Dynamics

Statistical Physics of Biomolecules: An Introduction by D. M. ZuckermanUnderstanding Molecular Simulation: From Algorithms to Applications, Second Edition by D. Frenkel and B. Smit Molecular Modelling: Principles and Applications (2nd Edition) by Andrew Leach

Selected Software for Molecular DynamicsSimulation Software DescriptionURLAMBER Assisted Model Building and Energy Refinement http://ambermd.org/ CHARMm Chemistry at HARvard Macromolecular Mechanics http://www.charmm.org/ GROMACS Groningen Machine for Chemical Simulations http://www.gromacs.org/ NAMD Scalable Molecular Dynamics www.ks.uiuc.edu/Research/namd/ Harry RichardsStephen EverseEthel StanleySandra OrchardGarby RusticiSam DonovanJohn JungckBert OverduinColleagues

Acknowledgments

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