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Vicky Choi Department of Computer Science Duke University

Protein Docking Plans for Local Improvement. Vicky Choi Department of Computer Science Duke University. Outline. Local Improvement Basic Idea Details of Each Step Current Results Work in Progress. “local”. Score:. Bump:. (b,s). (b,s). (a,r). (a,r).

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Vicky Choi Department of Computer Science Duke University

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  1. Protein Docking Plans for Local Improvement Vicky Choi Department of Computer Science Duke University

  2. Outline • Local Improvement • Basic Idea • Details of Each Step • Current Results • Work in Progress

  3. “local” Score: Bump: (b,s) (b,s) (a,r) (a,r) Protein Docking Problem (bound case)

  4. Local Improvement B A

  5. A A C B B Basic Idea

  6. 1.Compute Tentative Goal

  7. 2. Weighted Matching

  8. 3. Collision Resolution

  9. 3. Collision Resolution (Cont.)

  10. Example 1: 1BRS (patches) [Score, Bump]

  11. Example 2: 1BRS

  12. Example 3: 1BRS (non-docking site)

  13. Example 4: 1CHO

  14. Work in Progress A. varying neighborhood distance “D”; B. choosing the weights; C. trying jittering motions: C1. alternating between rotation and translation in pieces; C2. using a damping factor and iterating; D. adding hydrogens into the models.

  15. Protein Docking Group @Duke Pankaj K. Agarwal Sergei Bespamiatnykh Vicky Choi Herbert Edelsbrunner Abhijit Guria Johannes Rudolph Yusu Wang VMD – Visual Molecular Dynamics: http://www.ks.uiuc.edu/Research/vmd

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