Information
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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
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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 | |
| Intermezzo | ||||
| 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 | ||