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Daniel Russel and Leonidas Guibas Stanford University. Exploring Protein Folding Trajectories Using Geometric Spanners. Goals. Existing work understanding protein structure Classification Comparison Matching Qualitative understanding of proteins motions We do not quite get there yet. - PowerPoint PPT Presentation
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Exploring Protein Folding Trajectories Using Geometric
SpannersDaniel Russel and Leonidas Guibas
Stanford University
Goals
● Existing work understanding protein structure– Classification– Comparison– Matching
● Qualitative understanding of proteins motions– We do not quite get there yet
Geometric Spanners
● Vertexes are points● Edges have length● Expansion factor
– Ratio between graph distanceand Euclidean distance
Geometric Spanners
● Vertexes are points● Edges have length● Expansion factor
– Ratio between graph distanceand Euclidean distance
2CI2 Spanner
Expansion factor is 2Expansion factor is 2
backbone atom index
back
bon
e a
tom
ind
ex
spanner edges
2CI2 Spanner: Strands
parallel strands
antiparallel strands
backbone atom index
back
bon
e a
tom
ind
ex
Family of Descriptors
● Vary expansion factor ● From distance matrix to sparse● Linear for many values
1.5 1.75 2.0 2.5 3.0
Protein Folding Trajectories
● Input: Protein trajectories– Currently small proteins, later larger– Nanosecond timescales, later millisecond– Tens or hundreds of folding trajectories– Many non-folding
● Want to understand– Individual trajectories– Structure of conformation space
Processing Spanners
● Edges move slightly between frames● Tracked edge
initial frame edgesfinal frame edgesidentical edges
(identical edges colored grey or magenta)
some m
atching pairs
Smoothing
● Birth and death events● Persistent edges● Gaps
time
pers
iste
nt
ed
ges
Tracked edge
BirthDeath
Comparing Motions
● Compare pairs of trajectories– Partial matches
● Cluster conformations– Find bottlenecks
● Cluster trajectories– Which are similar– Which are unique