predicting protein folding paths - mathematicsmath.mit.edu/classes/18.417/slides/folding-prm.pdf ·...
TRANSCRIPT
![Page 1: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/1.jpg)
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Predicting Protein Folding Paths
Probabilistic Roadmap Planning (PRM):
Thomas, Song, Amato. Protein folding by motion planning.Phys. Biol., 2005
![Page 2: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/2.jpg)
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Protein Folding by Robotics
Probabilistic Roadmap Planning (PRM):
Thomas, Song, Amato. Protein folding by motion planning.Phys. Biol., 2005
![Page 3: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/3.jpg)
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Aims
Find good quality folding paths (into given nativestructure)
no structure prediction!
Predict formation orders (of secondary structure)
![Page 4: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/4.jpg)
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Motion planning
Motion planning
Probabilistic roadmap planing
Sampling of configuration space QConnect nearest configurations by (simple) local plannerApply graph algorithms to “roadmap”: Find shortest path
![Page 5: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/5.jpg)
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Motion planning
Motion planning
Probabilistic roadmap planing
Sampling of configuration space QConnect nearest configurations by (simple) local plannerApply graph algorithms to “roadmap”: Find shortest path
![Page 6: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/6.jpg)
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Motion planning
Motion planning
Probabilistic roadmap planing
Sampling of configuration space QConnect nearest configurations by (simple) local plannerApply graph algorithms to “roadmap”: Find shortest path
![Page 7: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/7.jpg)
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Motion planning
Motion planning
Probabilistic roadmap planing
Sampling of configuration space QConnect nearest configurations by (simple) local plannerApply graph algorithms to “roadmap”: Find shortest path
![Page 8: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/8.jpg)
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Motion planning
Motion planning
Probabilistic roadmap planing
Sampling of configuration space QConnect nearest configurations by (simple) local plannerApply graph algorithms to “roadmap”: Find shortest path
![Page 9: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/9.jpg)
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More on PRM for motion planning
tree-like robots (articulated robots)
Articulated Joint
configuration = vector of angles
configuration space
Q = {q | q ∈ Sn}
S — set of anglesn — number of angles = degrees of freedom (dof)
![Page 10: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/10.jpg)
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More on PRM for motion planning
tree-like robots (articulated robots)
configuration = vector of angles
configuration space
Q = {q | q ∈ Sn}
S — set of anglesn — number of angles = degrees of freedom (dof)
![Page 11: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/11.jpg)
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Proteins are Robots (aren’t they?)
Obvious similarity ;-)
==?
Our model
Protein == vector of phi and psi angles (treelike robotwith 2n dof)possible models range from only backbone up to full atom
![Page 12: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/12.jpg)
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Proteins are Robots (aren’t they?)
Obvious similarity ;-)
==?
Our model
Protein == vector of phi and psi angles (treelike robotwith 2n dof)possible models range from only backbone up to full atom
![Page 13: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/13.jpg)
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Proteins are Robots (aren’t they?)
Obvious similarity ;-)
==?
Our model
C
C C
C C
C
N
NN
O
O O
Protein == vector of phi and psi angles (treelike robotwith 2n dof)possible models range from only backbone up to full atom
![Page 14: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/14.jpg)
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Proteins are Robots (aren’t they?)
Obvious similarity ;-)
==?
Our model
C
C C
C C
C
N
NN
O
O O
phi psi
Protein == vector of phi and psi angles (treelike robotwith 2n dof)possible models range from only backbone up to full atom
![Page 15: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/15.jpg)
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Differences to usual PRM
no external obstacles, but
self-avoidingnesstorsion angles
quality of paths
low energy intermediate stateskinetically prefered pathshighly probable paths
![Page 16: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/16.jpg)
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Energy Function
method can use any potential
Our coarse potential[Levitt. J.Mol.Biol., 1983. ]
each sidechain by only one “atom” (zero dof)
Utot =∑
restraints
Kd{[(di − d0)2 + d2c ]
12 − dc}+ Ehp
first term favors known secondary structure through mainchain hydrogen bonds and disulphide bondssecond term hydrophobic effectVan der Waals interaction modeled by step function
All-atom potential: EEF1[Lazaridis, Karplus. Proteins, 1999. ]
![Page 17: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/17.jpg)
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PRM method for Proteins
Sampling Connecting Extracting
![Page 18: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/18.jpg)
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Sampling — Node Generation
Sampling Connecting Extracting
![Page 19: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/19.jpg)
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Node Generation
No uniform sampling
configuration space too large⇒ need biased sampling strategy
Gaussian sampling
centered around native conformationwith different STDs 5◦, 10◦, . . . , 160◦
ensure representants for different numbers of nativecontacts
Selection by energy
P(accept q) =
1 if E (q) < EminEmax−E(q)Emax−Emin
if Emin ≤ E (q) ≤ Emax
0 if E (q) > Emax
![Page 20: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/20.jpg)
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More on Node Generation
Visualization of Sampling Strategy
Distribution
Psi and Phi angles RMSD vs. Energy
![Page 21: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/21.jpg)
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Node Connection
Sampling Connecting Extracting
![Page 22: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/22.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 23: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/23.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 24: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/24.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 25: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/25.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 26: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/26.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 27: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/27.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
P1
P2
P3
P5
P4
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 28: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/28.jpg)
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
Weight
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 29: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/29.jpg)
S.W
ill,
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Connecting Nodes by Local Planner
connect configurations in close distance
generate N intermediary nodes by local planner
assign weights to edges
Pi =
{e−
∆EkT if ∆E > 0
1 if ∆E ≤ 0Weight =
N∑i=0
−log(Pi)
![Page 30: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/30.jpg)
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Extracting Paths
Sampling Connecting Extracting
![Page 31: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/31.jpg)
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Extracting Paths
Shortest Path
extract one shortest pathfrom some starting conformation, one path at a time
Single Source Shortest Paths (SSSP)
extract shortest paths from all starting conformationcompute paths simultaneouslygenerate tree of shortest paths (SSSP tree)
![Page 32: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/32.jpg)
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Big Picture
Sampling Connecting Extracting
![Page 33: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/33.jpg)
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Studied Proteins
Overview of studied proteins, roadmap size, andconstruction times
![Page 34: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/34.jpg)
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Formation orders
formation order of secondary structure for verifyingmethod
formation orders can be determined experimentally[ Li, Woodward. Protein Science, 1999. ]
Pulse labelingOut-exchange
prediction of formation orders
single pathsaveraging over multiple paths (SSSP-tree)
![Page 35: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/35.jpg)
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Timed Contact Maps
![Page 36: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/36.jpg)
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Formation Order
no (reported) contradictions between prediction andvalidation
different kind of information from experiment andprediction
![Page 37: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/37.jpg)
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The Proteins G and L
Studied in more detail
good test case
structurally similar: 1α + 4β
fold differently
Protein G: β-turn 2 forms firstProtein L: β-turn 1 forms first
![Page 38: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/38.jpg)
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Comparison of Analysis Techniquesβ-Turn Formation
![Page 39: Predicting Protein Folding Paths - Mathematicsmath.mit.edu/classes/18.417/Slides/folding-prm.pdf · Protein folding by motion planning. Phys. Biol., 2005. 2011 Aims Find good quality](https://reader036.vdocuments.site/reader036/viewer/2022071011/5fc922dc891d7d410b5ae568/html5/thumbnails/39.jpg)
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Conclusion
PRM can be applied to “realistic” protein models
Introduced method makes verifiable prediction
Coarse potential is sufficient
Predictions in good accordance to experimental data