Markov State Models. Gregory R. Bowman Miller Fellow University of California, Berkeley
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1 Markov State Models Gregory R. Bowman Miller Fellow University of California, Berkeley Tuesday, August 16, 2011
2 Defining The Protein Folding Problem
3 Defining The Protein Folding Problem
4 Why Mechanism?
5 Why Mechanism?
6 Why Mechanism?
7 The Sampling Challenge Bond vibration Isomerization Water dynamics Helix forms Fast folding Slow conf change protein oligomerization femto pico 10-9 nano 10-6 micro 10-3 milli 10 0 seconds 10 3 seconds MD step long MD run where we d love to be time on 1 fast CPU 1 day 3 years 3,000 years 3,000,000 years ~age of the earth Tuesday, August 16, 2011
8 The Sampling Challenge Bond vibration Isomerization Water dynamics Helix forms Fast folding Slow conf change protein oligomerization femto pico 10-9 nano 10-6 micro 10-3 milli 10 0 seconds 10 3 seconds MD step long MD run where we d love to be time on 1 fast CPU 1 day 3 years 3,000 years 3,000,000 years ~age of the earth Tuesday, August 16, 2011
9 The Sampling Challenge Bond vibration Isomerization Water dynamics Helix forms Fast folding Slow conf change protein oligomerization femto pico 10-9 nano 10-6 micro 10-3 milli 10 0 seconds 10 3 seconds MD step long MD run where we d love to be time on 1 fast CPU 1 day 3 years 3,000 years 3,000,000 years ~age of the earth Tuesday, August 16, 2011
10 The Sampling Challenge Bond vibration Isomerization Water dynamics Helix forms Fast folding Slow conf change protein oligomerization femto pico 10-9 nano 10-6 micro 10-3 milli 10 0 seconds 10 3 seconds MD step long MD run where we d love to be time on 1 fast CPU 1 day 3 years 3,000 years 3,000,000 years ~age of the earth Tuesday, August 16, 2011
11
12 Markov State Models (MSMs)
13 Markov State Models (MSMs)
14 Markov State Models (MSMs)
15 How to Build an MSM
16 How to Build an MSM
17 How to Build an MSM
18 Sample
19 Sample
20 Sample
21 Sample
22 Clustering Gives a High- resolution Model (this is a cartoon, since it s hard to draw 10,000 states in a talk) Tuesday, August 16, 2011
23 Lumping Provides Human Intuition
24 Under the Hood!"# $!"!% $!"& $'$ T(! t) =!"& $!"( $!"& $'$! $ $!"!) $!"* $'$ ' $ $' $ $' $ $'$!"#$%&#'&(&)"%&#'!"#'& Tuesday, August 16, 2011
25 Free Energy (kt) Modeling Experiments native state prediction Bowman, Beauchamp, Boxer, and Pande. JCP Bowman, Voelz, and Pande. JACS Tuesday, August 16, 2011
26 Free Energy (kt) Modeling Experiments native state prediction Bowman, Beauchamp, Boxer, and Pande. JCP Bowman, Voelz, and Pande. JACS Tuesday, August 16, 2011
27 Free Energy (kt) Modeling Experiments native state prediction!"#$%&#'&(&)"%&#'!"#'& Bowman, Beauchamp, Boxer, and Pande. JCP Bowman, Voelz, and Pande. JACS *+,"#'&(&!"#'!*+,& Tuesday, August 16, 2011
28 One Area Where We Need Help...
29 One Area Where We Need Help...
30 One Area Where We Need Help...
31 Jump- starting an MSM with Rosetta
32 Jump- starting an MSM with Rosetta
33 Jump- starting an MSM with Rosetta
34 What Can We Do For You?
35 What Can We Do For You? Dynamics in Design Tuesday, August 16, 2011
36 What Can We Do For You? Dynamics in Design Sampling Tuesday, August 16, 2011
37 What Can We Do For You? Dynamics in Design Sampling Force Field Assessment Tuesday, August 16, 2011
38 What Can We Do For You? Dynamics in Design Sampling Force Field Assessment? Tuesday, August 16, 2011
39 Conclusions
40 Conclusions Mechanism is important Tuesday, August 16, 2011
41 Conclusions Mechanism is important Markov state models are a powerful way of capturing the mechanisms of conformational change Tuesday, August 16, 2011
42 Conclusions Mechanism is important Markov state models are a powerful way of capturing the mechanisms of conformational change There s lots of room for collaboration! Tuesday, August 16, 2011
43 Thanks!
44 Conclusions Mechanism is important Markov state models are a powerful way of capturing the mechanisms of conformational change There s lots of room for collaboration! Tuesday, August 16, 2011
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