CS795 Tentative Syllabus


  • Instructor: Amarda Shehu amarda\AT\cs.gmu.edu
    Place and Time: ENT #276, R 7:20 - 10:00 pm
    Office Hours: T 4-6 pm

Tentative Topics

  • Modeling and Representation: Robot Kinematic and Molecular Chains
    Forward and Inverse Kinematics: Focus on Loop Closure
    Probabilistic Exploration: From Robot Motion Planning to Molecular Motions
    Enhanced Sampling of High-dimensional Spaces: Computing Native Protein Structures
    Protein-ligand and Protein-protein Docking: Rigid vs. Flexible
    Inter-molecular Association and Assembly: Molecular Complexes and Hierarchical Constructs

Tentative Syllabus

Date Topic Lecture Assignments Additional Reading
Sep. 03 Course Overview, Introduction Lecture 1 [pdf]   [m1] Chapter
Modeling and Kinematics
Sep. 10 Modeling, Forward Kinematics Lecture 2 [pdf] [ppt] Hw1 Out [html] [m2] DH derivation [m3]
Sep. 17 Inverse Kinematics Lecture 3 [pdf] [ppt]   [m4] Baxter Dunbrack
Sep. 24 Loop Modeling Lecture 4 [ppt]   Buss Lotan Shehu
Probabilistic Exploration: From Robot to Molecular Motion Planning
Oct. 01 Sampling-based Motion Planning Lecture 5 [pdf] Hw1 Due Guest Lecturer:
Erion Plaku
Oct. 08 Roadmap Methods in Biology Lecture 6 [ppt] Hw2 Out [pdf] [m5] [m6]
Enhanced Sampling for Computing Protein Native Structures
Oct. 15 Trajectory-based Exploration Lecture 7 [ppt]   Shehu Review [m7] Survey article
Oct. 22 Fragment-based Assembly Lecture 8 [ppt] Hw2 Due  
Oct. 29 Research Article Highlight Lecture 9 [ppt] Select Project Shehu RSS 09
Docking Molecules
Nov. 05 Docking Ligands and Proteins Lecture 10 [ppt] Hw3 Out [pdf] [m8] [Geom. Hashing]
Nov. 12 Complex Assembly Lecture 11 [ppt]   Bailey-Kellogg 07
Student Presentations of Research Articles
Nov. 19 Class Presentations   Hw3 Due Reading and Presenting
Nov. 26 Thanksgiving break      
Select Topics
Dec. 03 Structure Comparison Lecture 12 [ppt] Progress Report Due Zemla LGA 03
Dec. 10 Project Presentations   Final Report Due