CPSC 689-608

Special Topics in Motion Planning

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Meeting Place: HRBB 407
Class time:  2pm to 4pm TR

                  (01/24)  Potential and Potential landcape concept in Protein Folding
                     1) class notes (ppt).
                     2) paper on protein folding lanscape and funnels.
                  Assignment due:  a report on the paper 2).
 

         Week 2:
                  (01/29)  Motion Planning Approach to Folding Problems
                    1)  paper 1: A motion planning approach to Folding: From paper craft to protein folding
                    2)  paper 2: Using motion planning to Study protein folding pathways
                          (note: you should be able to find both papers by following the above links.)
                    3)  class notes (ppt presentation notes)
                 Assignment due:  a summary report on both papers.
 

                 (01/31)  Protein Structure Prediction.
                    1) Reading:  Chapter 1 of   "Protein Structure Prediction" (Reference 1)
                    2) class notes (ppt)
                 Assignment due:  a summary report.
                 Quiz II.

         Week 3:
                 (02/05) Ligand Binding.
                     1) paper:  Ligand Binding with OBPRM and Haptic Input (Burchan)
                     2) power point presentation (ppt)
                  Assignment due: a summary report.

                  (02/07) Thermodynamics and Dynamics of Protein Folding: Approches.
                       Diffusion Collision Model;  Molecular Dynamics simuation; Lattice Model; Monte
                        Carlo simulation;  (For more out-of-class reading: check out the suggest reading page.)

                      1) Reading:  hard copy is available in 407B starting this Monday, also in class Tuesday.
                             Chapter 4 of Reference 2: "Protein Folding:Theoretical studies of Thermodynamics and Dynmics."
                             Chapter 28 of Reference 3. "The diffusion-collision model of Protein Folding"
                      2) class notes (was on board:-)
                   Assignment due: a summary report Thurday in class.
 

         Week 4:
                (02/12) Shawna's research presentation
 
                (02/14) Lattice model. Kinetics of Protein Folding (I)
                    Free Energy concept; entropy;
                    Intermediate state, transition state; Transition State Theory (TST), Kramers' Theory;
 
                    1) Read: Chapter 4 of Reference 4.
                                  Chapter 16 of Reference 3.
                        hard copy available in  class or Rm 407.
                    2) class notes (ppt)

         Week 5:
                (02/17)

                (02/21)  Kinetics of Protein Folding (II)
                    2-state folding kinetics; folding rate; statistical model.
                    PRM new stuff on Protein Folding
 
               1) Reading:
                    Paper 1: A simple model for calculating the kinetics of protein folding...
                    Paper 2: Using motion planing to map protein folding landscape and analyze folding kinetics..
 

References:
1. Protein Structure Prediction, a practical approach. Edited by Michael J. E. Sternberg
2. Protein Folding. T.E. Creighton. 1994
3. Protein Folding: the deciphering the second half of genetic code. Edited by Gierasch and King, 1990
4. Protein Folding kinetics, B. Nolting. 1999
5. Folding research page in our group.

Helpful links:
1) suggest reading on protein folding,  drug docking, computational methods.