Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.
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Transcript of Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.
Using Pseudotorsions to Predict the Consensus Rotamers
Kevin Keating
Yale University
What are Pseudotorsions?
What are Pseudotorsions?
Clustering
C3’ endo C2’ endo
Clustering
C3’ endo C2’ endo
Clustering
C3’ endo
Comparing with RMSD
Comparing with RMSD
Structure Building
Structure Building
Problem 1: Nucleotide vs. Suite
Problem 1: Nucleotide vs. Suite
Problem 2: Locating C4’
Problem 2: Locating C4’
From Pseudotorsions to Rotamers
C2’-C3’ puckersUsing C4’
From Pseudotorsions to Rotamers
C2’-C3’ puckersUsing C1’
How to Determine Pucker
C2’ endo
C3’ endo
How to Determine Pucker
(Developed by Richardson lab)
How to Determine Pucker
(Developed by Richardson lab)
How to Determine Pucker
How to Determine Pucker
Putting It (Almost) All Together
Non-helical Suites
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
1 2 3 4 5 6 7 8 9 10 >10Rotamer Rank
Per
cen
tag
e C
orr
ect
Putting It (Almost) All Together
Helical Suites
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
1 2 3 4 5 6 7 8 9 10 >10Rotamer Rank
Per
cen
tag
e C
orr
ect
Distances
Distances
C3’-C2’ puckers only
Distances
4 5 6 7 8 9 10
C1'-C1' Distance (Å)
Sm
oo
the
d D
istr
ibu
tion
1[
1b
1o
1t
1z
3b
5z
7p
7r
Putting It All Together
Non-helical Suites
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
1 2 3 4 5 6 7 8 9 10 >10Rotamer Rank
Per
cen
tag
e C
orr
ect
Putting It All Together
Helical Suites
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
1 2 3 4 5 6 7 8 9 10 >10Rotamer Rank
Per
cen
tag
e C
orr
ect