Biomolecular Modeling
General Course Information:
HI 6327 Biomolecular Modeling
UCT 1414
Meeting day: Wednesday
Meeting time: 5-8PM
Instructor Information:

Willy R Wriggers
Associate Professor
Office Address: 7000 Fannin, Suite 1480
Telephone Number: 713-500-3961
Fax Number: 713-500-3907
E-mail: wriggers >>at<< biomachina.org
Office Hours: 2 hours before class

Reading Materials:
Required
  • Tamar Schlick "Molecular Modeling and Simulation" (Springer Verlag, 2002)
  • Philip E. Bourne and Helge Weissig "Structural Bioinformatics" (Wiley, 2003)
    Recommended
  • Leach "Molecular Modeling: Principles and Applications" 2nd edition (Prentice Hall, 2001)
  • Brooks, Karplus, Pettitt "Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics" (Wiley, 1990)
  • Lesk "Introduction to Protein Architecture" (Oxford U Press, 2001)

    		•
    Course Description
    This course provides a broad and practical introduction to the major techniques employed in the computational modeling of biological structures: computational chemistry, molecular dynamics, normal mode analysis, Monte Carlo simulations, electrostatics, and conformational analysis. The course will be useful for graduate students in the pharmaceutical and medical disciplines who wish to model the physical and chemical properties of biological structures.
    Prerequisites
    Background in at least one quantitative discipline (physics, chemistry, mathematics, computer science) at college level. Knowledge of at least one programming language. Scientific curiosity and imagination. Good writing skills. Interest in the crossing of boundaries between traditional scientific disciplines.
    Course Objectives
    By the end of the semester, the student will have had the opportunity to meet the following objectives:
    1. Characterize the role of biomolecular modeling in concurrent pharmaceutical research, and in cell and structural biology.
    2. Describe the functionality, advantages, and limitations of standard computing strategies for the simulation of biomolecules.
    3. Acquire a working knowledge of freely available software to carry out independent research projects in biomolecular modeling.
    4. Explore the possibilities for modeling to assist in the process of determination, analyzing, evaluating, displaying, and retrieving of 3D structura data in a research or industry laboratory environment.
    5. Develop pieces of software and computer scripts that serve as template for own future research work.
    Method of Instruction
    Lectures
    Reading
    Homework Assignments
    Hands-On Training Sessions
    Group Activities
    Method of Evaluation
    Howework assignments (Individual) 35%
    • Two take-home programming or problem solving assignments (about 5-8 hours each)

    Method evaluation assignment (Group) 25%

    • Groups of students (per agreement) evaluate a chosen modeling method 
    • Propose solutions to identified problems
    • 5 page group paper focusing on suitability and limitations
    Final Exam Project and Term Paper (Individual) 40%
    • Carry out "bite-sized" modeling or simulation project (must select a project by mid term in agreement with instructors)
    • Submit 5-8 page report written in classic manuscript style (abstract, introduction, methods, results, discussion)
    • Evaluation criteria: Complexity of project, demonstrated competence, quality of paper.
    • May re-use material from previous assignments.
    Note:      Submissions and paper are needed in CBE format; if not, at least one letter grade will be deducted.  Check your local library and book store for a copy of "Scientific Style and Format", Council of Biology Editors, Inc., 6th ed. Cambridge University Press.
    Laptop Computer Requirement
    Each student must have their own computer for class.   Recommended computer requirements
    Recommended monitor resolution: 1024 X 768 Screen Area or higher, High Color - 16bit or higher
    High speed line: DSL or Cable  is recommended
    Topical Outline (topics in light gray are preliminary)
    Wed 01/10/07 Session 1 Molecular Modeling Overview Reading-Assignment
    Wed 01/17/07 Session 2 Biomolecular Structure, UNIX I
    		 Preparations Reading
    Wed 01/24/07 Session 3 Visualization of Biomolecular Structures, UNIX II
    		 Homework 1: due @ session 5
    Wed 01/31/07 Session 4 Molecular Dynamics Simulation: Overview, Practice I
    		 Reading Assignment
    Wed 02/07/07 no class (office hours by agreement)
    Wed 02/14/07 Session 5 Molecular Dynamics Simulation: Practice II Homework 2: due @ session 7
    Wed 02/21/07 Session 5 (catching up)
    		 Solutions HW1
    Wed 02/28/07 Session 6 Molecular Dynamics Simulation: Preparation, Analysis
    Wed 03/07/07 no class
    		 (Spring Break / Biophysical Society Meeting)
    Wed 03/14/07 Session 7 Normal Mode and Principal Component Analysis
    		 Solutions HW2
    Wed 03/21/07 Session 8 Thermodynamics, Monte Carlo, Continuum Electrostatics Group Project: due @ session 11
    Wed 03/28/07 Session 9 Free Energy Calculations
    Wed 04/04/07 Session 10 Ligand Binding, Docking, and Screening
    		 Term Project: due @ session 14
    Wed 04/11/07 Session 11 Quantum Chemistry I
    Wed 04/18/07 Session 12 Quantum Chemistry II
    Wed 04/25/07 Session 13 Multi-Scale Modeling
    Wed 05/02/07
    		 Session 14
    		 (no class - term paper due)

    Excused Absence on Holy Days
    Absence from any class or excuse for a late assignment or test/quiz/examination because the date is a holy day will be permissible only if the form for holy day absence, available from the Office of Academic Affairs (UCT600), has been completed by the student and the instructor, and submitted by the student to the Office of Academic Affairs within the first 15 days of the semester. Documentation of a holy day, other than well-known holy days in the community, by a religious official also is required.
    Intellectual Propert

    Information on intellectual property issues may be found at http://www.utsystem.edu/OGC/IntellectualProperty/ippol.htm