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.
![Page 1: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/1.jpg)
Using Pseudotorsions to Predict the Consensus Rotamers
Kevin Keating
Yale University
![Page 2: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/2.jpg)
What are Pseudotorsions?
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What are Pseudotorsions?
![Page 4: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/4.jpg)
Clustering
C3’ endo C2’ endo
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Clustering
C3’ endo C2’ endo
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Clustering
C3’ endo
![Page 7: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/7.jpg)
Comparing with RMSD
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Comparing with RMSD
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Structure Building
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Structure Building
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Problem 1: Nucleotide vs. Suite
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Problem 1: Nucleotide vs. Suite
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Problem 2: Locating C4’
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Problem 2: Locating C4’
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From Pseudotorsions to Rotamers
C2’-C3’ puckersUsing C4’
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From Pseudotorsions to Rotamers
C2’-C3’ puckersUsing C1’
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How to Determine Pucker
C2’ endo
C3’ endo
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How to Determine Pucker
(Developed by Richardson lab)
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How to Determine Pucker
(Developed by Richardson lab)
![Page 20: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/20.jpg)
How to Determine Pucker
![Page 21: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/21.jpg)
How to Determine Pucker
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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
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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
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Distances
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Distances
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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
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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
![Page 28: Using Pseudotorsions to Predict the Consensus Rotamers Kevin Keating Yale University.](https://reader038.fdocuments.us/reader038/viewer/2022110323/56649d605503460f94a40e25/html5/thumbnails/28.jpg)
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