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Gibbs sampling Morten Nielsen, CBS, BioSys, DTU. Class II MHC binding MHC class II binds peptides in the class II antigen presentation pathway Binds peptides.

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Presentation on theme: "Gibbs sampling Morten Nielsen, CBS, BioSys, DTU. Class II MHC binding MHC class II binds peptides in the class II antigen presentation pathway Binds peptides."— Presentation transcript:

1 Gibbs sampling Morten Nielsen, CBS, BioSys, DTU

2 Class II MHC binding MHC class II binds peptides in the class II antigen presentation pathway Binds peptides of length 9-18 (even whole proteins can bind!) Binding cleft is open Binding core is 9 aa

3 Gibbs sampler mer peptides ~10 30 combinations Monte Carlo simulations can do it

4 Gibbs sampler. Monte Carlo simulations RFFGGDRGAPKRG YLDPLIRGLLARPAKLQV KPGQPPRLLIYDASNRATGIPA GSLFVYNITTNKYKAFLDKQ SALLSSDITASVNCAK GFKGEQGPKGEP DVFKELKVHHANENI SRYWAIRTRSGGI TYSTNEIDLQLSQEDGQTIE RFFGGDRGAPKRG YLDPLIRGLLARPAKLQV KPGQPPRLLIYDASNRATGIPA GSLFVYNITTNKYKAFLDKQ SALLSSDITASVNCAK GFKGEQGPKGEP DVFKELKVHHANENI SRYWAIRTRSGGI TYSTNEIDLQLSQEDGQTIE E1 = 5.4 E2 = 5.7 E2 = 5.2 P accept =1 0 < P accept < 1

5 Monte Carlo Temperature What is the Monte Carlo temperature? Say dE=-0.2, T=1 T=0.001

6 Shift alignment window Gibbs sampler. Monte Carlo simulations Getting stucked in local minima

7 It works High TemperatureLow Temperature

8 Gibbs sampler. Prediction accuracy

9 Use of Gibbs sampling More than 1,000 papers in PubMed using Gibbs sampling methods Transcription start-sites Receptor binding sites Acceptor:Donor sites...

10 Summary Weight matrices can accurately describe a sequence motif like MHC class I Use sequence weighting to remove data redundancy Use pseudo count to compensate for few data points Gibbs sampling can detect MHC class II binding motif


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