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Introduction to Computational Biology: Curriculum Development Ruijun ZhaoKai ShenShaneka Simmons Presented by:

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1 Introduction to Computational Biology: Curriculum Development Ruijun ZhaoKai ShenShaneka Simmons Presented by:

2 CREATING THE CURRICULUM FOR COMPUTATIONAL BIOLOGY 1

3 QUESTIONS CONSIDERED FOR EFFECTIVE COURSE DESIGN 1.What students will you target and what are their needs? 2.What do you want them to learn? 3.What content matter will engage the students? 4.What will your students discover about the class that they can relate to everyday life? a.Drug design b.Enzyme modification c.Food Industry 5.What are your strengths put into this course? 6.Teach students how to identify and solve problems? 7.Teach students how to utilize modern tools and promote current topics of interest? 8.Who will be your collaborators (invited speakers, course development)

4 3 Course Objectives Brainstorm

5 Shaneka 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

6 Curriculum 4

7 Course Objectives 1.Students will be able to set up, run a simulation and interpret the simulation results through case studies. 2.Students will be able to utilize mainstream bioinformatics tools. 3.Students learn to effectively collaborate with their peers.

8 Student Preliminary Assessment Foldit game at the introduction of the class and after the introduction to molecular dynamics Homework assignments – Concept understanding – Justification of protein selection Group projects – Exploring tools and solve a real problem What is the structure-function relationship Proteopedia (www.proteopedia.org) – Math Scoring using Protein Docking

9 Future Work Design modules – Video modules – Powerpoint presentations – Source files for community utilization – Introductory teaching tutorials for students Design online courses

10 Why should we care? Conveying: Introduction to Computational Biology http://www.ebi.ac.uk/ luscombe/docs/ imia_review.pdf

11 5 SAMPLE COURSE TOPICS

12 Module 1: Protein Structures-Basic Introduction Chemical bonds, weak forces involved in protein structures Amino acids, primary structures, secondary, and tertiary structures Side chains of protein residues, protein- protein/protein-ligand interaction

13 Module 2. Molecular Visualization Visualization software DescriptionURL PDBeEBI's Protein Data Bank in Europe http://www.ebi.ac.uk/pdbe/ PDBRCSB’s database of proteinhttp://www.pdb.org/ PyMOLMolecular visulization softwarehttp://www.pymol.org JMolOpen source Java Viewer for 3D structures http://jmol.sourceforge.net VMDMolecular visualization and dynamics software www.ks.uiuc.edu/Research/vmd/

14 Module 3. Protein Docking Principles of Docking – Review interactions, chemical bonds, and protein structures – Search algorithm – Scoring functions Working with docking software suits with a focus on open source packages – HADDOCK, AUTODOCK, ZDOCK, etc. Application – Drug discovery Tutorial http://ringo.ams.sunysb.edu/index.php/2012_DOCK_tutoria l_with_Streptavidin

15 Docking Software Packages

16 Module 4: Molecular Dynamics

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

18 Selected Software for Molecular Dynamics Simulation Software DescriptionURL AMBERAssisted Model Building and Energy Refinement http://ambermd.org/ CHARMmChemistry at HARvard Macromolecular Mechanics http://www.charmm.org/ GROMACSGroningen Machine for Chemical Simulations http://www.gromacs.org/ NAMDScalable Molecular Dynamicswww.ks.uiuc.edu/Research/na md/

19 Harry Richards Stephen Everse Ethel Stanley Sandra Orchard Garby Rustici Sam Donovan John Jungck Bert Overduin Colleagues Acknowledgments


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