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Messages - Puru@1998
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1
« on: July 04, 2018, 11:40:08 pm »
Hello.
I was wondering if you had a response regarding my post above.
Thanks.
2
« on: June 22, 2018, 01:26:17 pm »
Hello. Thank you for your responses.
I will clarify my questions to the best of my ability.
I am trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B) ..in this manner. I was wondering if 3dna has a way of accomplishing this without me having to do it manually say for a database of 300 structures of DNA/DNA and RNA/RNA duplexes that I have created.
Examples: step Xp Yp Zp XpH YpH ZpH Form
1 GG/CC -2.93 8.97 0.37 -3.31 8.93 0.93 B
2 GT/AC -3.35 9.11 -0.39 -4.65 9.11 0.27 B
3 TG/CA -2.75 8.65 -0.88 0.06 8.42 -2.19 B
4 GC/GC -3.75 8.88 -1.02 -4.46 8.86 1.15 B
5 CA/TG -2.21 8.39 -0.80 0.87 8.11 -2.24
6 AA/TT -3.16 8.72 -0.76 -3.15 8.69 -1.08 B
7 AC/GT -3.34 8.80 0.30 -4.58 8.79 -0.36 B
8 CA/TG -3.15 8.59 0.82 -5.42 7.85 3.62
9 AA/TT -3.40 8.91 -0.05 -5.18 8.77 1.57 B
10 AA/TT -2.85 9.21 0.49 -4.46 8.93 2.31 B
11 AT/AT -2.73 9.23 0.37 -5.90 8.10 4.48
12 TT/AA -3.06 8.49 0.75 -7.77 2.66 8.09
13 TG/CA -1.93 8.53 -1.20 -1.73 8.42 1.80
14 GA/TC -3.71 8.29 -1.70 -1.39 8.33 -1.77
15 AT/AT -3.33 8.91 0.01 -3.85 8.89 -0.62 B
16 TA/TA -3.07 8.68 0.30 -3.26 8.62 -1.09 B
17 AA/TT -3.23 8.99 -0.12 -3.62 8.93 -1.05 B
18 AG/CT -2.99 8.80 -0.12 -4.25 8.76 0.81 B
19 GC/GC -2.88 8.98 -0.05 -2.91 8.98 -0.13 B
20 CA/TG --- --- --- --- --- --- ---
21 AA/TT --- --- --- --- --- --- ---
22 AT/AT -1.31 5.67 -0.75 -1.12 5.67 -0.38
23 TG/CA -3.05 9.04 -0.43 -1.94 9.05 -0.15 B
24 GC/GC -3.22 9.12 -0.18 -3.87 9.12 0.02 B
25 CT/AG -3.15 8.71 0.12 -4.40 8.67 0.80 B
26 TT/AA -3.20 9.07 -0.14 -3.66 9.01 -1.00 B
27 TT/AA -3.31 9.00 -0.28 -4.03 9.00 -0.28 B
28 TT/AA -3.32 8.90 -0.38 -3.06 8.75 -1.69 B
29 TT/AA -2.84 8.83 -0.02 -2.70 8.77 -0.99 B
30 TT/AA -3.17 8.80 -0.39 -4.01 8.81 -0.16 B
31 TG/CA -2.68 8.86 -0.39 -2.17 8.73 1.56 B
32 GG/CC -2.62 8.93 0.55 -4.88 8.43 3.01
33 GC/GC -3.01 9.06 0.57 -4.46 8.93 1.66
About 63 percent B so, B- Like
Structure 1ihf.pdb
step Xp Yp Zp XpH YpH ZpH Form
1 Ug/gA -0.59 1.90 -10.29 -1.26 -5.96 -8.21
2 gg/gg -0.03 11.87 -0.05 -0.04 11.87 -0.05
3 gA/Ug 4.30 6.48 0.76 4.86 6.47 0.71
4 AG/GU --- --- --- --- --- --- ---
5 GA/UG --- --- --- --- --- --- ---
6 AG/GU --- --- --- --- --- --- ---
7 GA/UG 0.91 7.95 -3.89 0.95 7.96 -3.89
8 AU/AU --- --- --- --- --- --- ---
9 UG/GA 4.86 -3.16 -3.09 3.46 -5.61 -2.45
10 GG/GG 2.86 -8.07 9.47 0.69 -11.79 7.22
11 GU/UG -0.70 -5.57 0.33 -0.39 -5.58 -0.02
12 UA/UU 4.87 4.65 9.91 6.37 4.62 8.66
13 Ag/gU --- --- --- --- --- --- ---
14 gU/Ag --- --- --- --- --- --- ---
15 UG/GA 4.76 -3.15 -3.07 3.40 -5.68 -2.41
16 GU/UG -0.69 -0.62 3.16 3.87 0.05 -5.38
17 UG/GU -1.13 9.00 12.68 -1.60 9.15 12.56
18 GU/UG -2.66 2.33 7.98 -3.11 -1.49 5.97
19 UA/UU 1.44 7.36 8.41 1.48 7.36 8.39
20 Ag/gU --- --- --- --- --- --- ---
21 gG/Gg -1.88 -0.50 6.72 -3.52 -0.95 6.73
22 GG/GG 2.93 -8.32 9.69 0.64 -11.88 7.20
23 GU/UG -0.93 -5.19 0.60 -0.36 -5.24 0.05
(this structure has x on for a step without a continuous backbone- from the DSSR output; 3dna just leaves them blank)
step Xp Yp Zp XpH YpH ZpH Form
1 ga/TC -2.77 8.59 0.69 -3.28 8.62 0.28
2 ac/GT -2.49 8.71 1.70 -4.62 8.57 2.22
3 ca/TG -3.29 8.69 1.01 -7.71 7.93 3.84
4 ac/GT -3.02 9.01 1.11 -8.02 8.96 1.50
5 cc/GG -1.93 8.22 2.51 -5.41 7.78 3.66 A
6 cu/AG -2.26 8.95 1.99 -6.31 9.06 1.61 A
7 ug/CA -2.51 8.67 1.19 -4.74 8.70 1.07
8 ga/uC -2.43 8.87 1.41 -6.30 7.97 4.14
9 au/Au -2.90 8.63 0.53 -5.39 8.55 1.15
10 uu/AA -2.76 8.87 1.25 -8.18 8.07 3.92
11 uc/GA -2.38 8.52 1.92 -5.00 8.39 2.38
9 percent A..?
3DNA has been incredible to use so far, very multi-dimensional and comprehensive.
Thank you.
3
« on: June 19, 2018, 03:42:05 pm »
Hello
I have been working on RNA/DNA hybrids with conformational parameters, along with DNA and RNA duplexes.
I was wondering if there is a script , another way to classify the structures that I have compiled by A, B, AB, TA- type( which is done and seen on the forum)?
Sincerely,
Puru
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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University
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