Molecular Modeling in Bioinformatics (BioE 483)
This course teaches the students how to elucidate the structure of a biopolymer using related modeling tools and algorithms in bioinformatics. The targeted areas are in protein structure modeling, structure based drug design, drug screening, cheminformatics, and binding prediction. Students will learn the principles and applications of each of the algorithms and programs used in structure modeling.
Topics covered and software used:
- Protein-ligand (drug) binding: DOCK, AUTODOCK
- General packages aimed at structure modeling: SYBYL, QUANTA, INSIGHT II
- Molecular dynamics simulations: CHARMm, AMBER
Syllabus:
- Lecture 1: Introduction
- Lecture 2: Molecular Mechanical Force Field (1)
- Lecture 3: Molecular Mechanical Force Field (2)
- Lecture 4: Statistical Potentials (1)
- Lecture 5: Statistical Potentials (2)
- Lecture 6: Conformational Analysis (1)
- Lecture 7: Conformational Analysis (2)
- Lecture 8: Minimization
- Lecture 9: Computer simulation
- Lecture 10: Monte Carlo simulation
- Lecture 11: Molecular Dynamics Simulation (1)
- Lecture 12: Molecular Dynamics Simulation (2)
- Lecture 13: Structure Modeling (1)
- Lecture 14: Structure Modeling (2)
- Lecture 15: Structure Modeling (3)
- Lecture 16: Structure Modeling (4)
- Lecture 17: Structure Modeling (5)
- Lecture 18: Structure Modeling (6)
- Lecture 19: Protein interactions
- Lecture 20: Free energy calculation
- Lecture 21: Drug design
- Lecture 22: Special topics
We will normally post 2 lectures per week (on Mondays).
Prerequisites:
- Calculus: Basic knowledge
Example: Integration-differential calculus, functional analysis, the meaning of first and second derivatives, basic knowledge of differential equations. - Linear Algebra: Basic knowledge
Example: Matrices, what they represent and basic operations, i.e. matrix addition, multiplication, transposition, inversion, knowledge of vector operations. - Programming: Basic knowledge of either Matlab, C/C++, Perl, Java, etc. Visual Basic and Delphi are acceptable.
Example:Students should be able to open and read text files, extract data from those files, transfer the data from text format to numeric format and manipulate then using mathematical functions, and finally save the results as either text files or binary files. - Physics: High school physics or physics 101
Example:Students should know the difference between force and energy, the dependence of force on acceleration, equation of motion, the coordinate system, etc. - Chemistry and Biology: Chemistry background, BioE 480 or similar course
Example:Students should know basic properties of nucleic acids (DNA and RNA), and properties of amino acids (20 natural amino acids which form proteins).
Textbook:
Leach, A., Molecular Modelling: Principles and Applications, Second Edition, Prentice Hall, ISBN-10: 0582382106, ISBN-13: 978-0582382107
Grading:
- Homework
- worth 100 points will be assigned each week.
- The homework will be posted on Wednesday and will be due the following Wednesday.
- For any week, we may post homework early. This will not affect the due date of the homework.
- Late homework will be accepted until the first Friday following the due date with a penalty of 20 points per day late. Homework will not be accepted after Friday.
- Comprehensive project (due on the same day as the final exam)
- Midterm and final exams