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CS273 Final Project Stephane Laidebeure

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Presentation on theme: "CS273 Final Project Stephane Laidebeure"— Presentation transcript:

1 CS273 Final Project Stephane Laidebeure
Protein design CS273 Final Project Stephane Laidebeure

2 CS273: Protein design algorithms Stephane Laidebeure
Problem to solve What is protein design? The molecular model Algorithms Monte-Carlo algorithm Dead-end elimination Further work CS273: Protein design algorithms Stephane Laidebeure

3 The problem: what are we trying to design?
EEEQTALVCD NGSGLVKAGF AGDDAPRAVF PSIVRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE HGIITNWDDM EKIWHHTFYN ELRVAPEEHP VLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVSHN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FEQEMATAAS SSSLEKSYEL PDGQVITIGN ERFRGPETMF QPSFIGMESS GVHETTYNSI MKCDIDIRKD LYANNVLSGG TTMYPGIADR MQKEITALAP STMKIKIIAP PERKYSVWIG GSILASLSTF QQMWITKQEY DESGPSIVHR KCF CS273: Protein design algorithms Stephane Laidebeure

4 CS273: Protein design algorithms Stephane Laidebeure
The molecular model Rigid sticks Free rotation around the axes… … but not around the knees “Natural” distances and angles CS273: Protein design algorithms Stephane Laidebeure

5 CS273: Protein design algorithms Stephane Laidebeure
The molecular model Rigid sticks Energy model Distances between bounded atoms Distances between non-bounded atoms Angles d a d0 CS273: Protein design algorithms Stephane Laidebeure

6 Model for protein design
Modeling the chain and the sticks Chain structure Stick structure Affecting slots on the chain Computing the energy efficiently Independent and pairwise terms Caching the values CS273: Protein design algorithms Stephane Laidebeure

7 Algorithms for protein design
Monte-Carlo methods Description Greedy vs simulated annealing Random restart Dead-end elimination Description Precomputing the matrix Selecting candidate rotamers Backtracking CS273: Protein design algorithms Stephane Laidebeure

8 CS273: Protein design algorithms Stephane Laidebeure
Further work Modifying the chain and stick generation Introducing a notion of neighborhood between slots in the chain Trying new heuristics for selecting the candidates Combining the two methods CS273: Protein design algorithms Stephane Laidebeure

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