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