FOLDNOX: Finding Of Labeled 3-D Structure Based On NOX Distances

Creating Matlab Scripts

Create Matlab Scripts Using comb.in
predicted DNA 4-W junction

Building Structures

Build Structures Using matlab.res

Instructions

Here are some basic instructions about how to create scripts and how to build structures. Example comb.in

Examples

Case Description Lowest Dist-RMSD (Structure-RMSD) Lowest Structure-RMSD (Dist-RMSD) Lowest Structure-RMSD among first 10 clusters (with Dist-RMSD) Time of Running (hrs)
01 planar-DNA 3-way junction(3p-3d-9fixdist/err0) 0.006 (5.1) 1.77 (0.011) 2.12 (0.007) 1.87
02 planar-DNA 3-way junction (3p-3d-9vardist/err0) 0.003 (12.7) 4.06 (0.020) 11.84 (0.006) 1.88
03 planar-DNA 3-way junction (3p-3d-9vardist/err3) 0.694 (12.9) 4.02 (2.374) 8.99 (1.158) 1.75
04 planar-DNA 3-way junction (3p-3d-9vardist+/err3) 1.236 (7.96) 1.38 (2.447) 7.96 (1.236) 1.46
05 planar-DNA 3-way junction (3p-3d-9vardist-/err3) 0.569 (10.85) 4.56 (2.448) 10.85 (0.569) 1.45
06 planar-DNA 3-way junction (3p-4d-12fixdist/err0) 0.002 (1.12) 0.019 (0.90) 0.99 (0.007) 1.50
07 planar-DNA 3-way junction (3p-4d-12vardist/err0) 0.016 (15.9) 3.30 (0.046) 9.62 (0.023) 1.55
08 planar-DNA 3-way junction (3p-4d-12vardist/err3) 1.123 (13.22) 4.71(1.256) 3.27 (2.111) 1.55
09 planar-DNA 3-way junction (3p-4d-12vardist+/err3) 0.956 (9.66) 0.532 (2.121) 2.7 (1.46)
10 planar-DNA 3-way junction (3p-4d-12vardist-/err3) 1.087(15.47) 3.49 (2.121) 12.56 (1.146)
11 planar-DNA 3-way junction(3p-5d-15fixdist/err0) 0.016 (0.532) 0.502 (0.021) 0.502 (0.021)
12 planar-DNA 3-way junction(3p-5d-15vardist/err0) 0.048(14.33) 4.19 (0.064) 4.23 (0.062)
13 planar-DNA 3-way junction(3p-5d-15vardist+-/err3) 0.048 (17.31) 2.07 (1.536) 9.23 (0.062)
14 planar-DNA 3-way junction(3p-5d-15vardist+/err3) 0.048(15.36) 0.51 (0.183) 15.20 (0.062)
15 planar-DNA 3-way junction(3p-5d-15vardist-/err3) 1.190 (14.15) 3.56 (1.763) 9.73 (1.273)
16 Non-planar-DNA 3-way junction(3p-3d-9fixdist/err0) 0.003 (11.88) 2.07 (0.009) 5.08 (0.005)
17 Non-planar-DNA 3-way junction(3p-3d-9vardist/err0) 0.004 (16.54) 4.97 (0.008) 6.61 (0.005)
18 Non-planar-DNA 3-way junction(3p-3d-9vardist/err3) 1.413 (16.77) 3.30 (2.338) 7.7 (1.508)
19 Non-planar-DNA 3-way junction(3p-3d-9vardist+/err3) 1.271 (10.4) 1.29 (2.450) 10.4 (1.271)
20 Non-planar-DNA 3-way junction(3p-3d-9vardist-/err3) 1.248 (14.24) 3.59 (1.321) 13.59 (2.350)
21 Non-planar-DNA 3-way junction(3p-4d-12fixdist/err0) 0.003 (11.34) 0.714 (0.006) 0.714 (0.006)
22 Non-planar-DNA 3-way junction(3p-4d-12vardist/err0) 0.022 (15.9 ) 6.4 (0.048) 12.8 (0.027)
23 Non-planar-DNA 3-way junction(3p-4d-12vardist/err3) 0.706 (7.07) 3.61 (1.962) 6.80 (0.925)
24 Non-planar-DNA 3-way junction(3p-4d-12vardist+/err3) 0.656 (11.98) 0.722 (1.059) 310 (2.123)
25 Non-planar-DNA 3-way junction(3p-4d-12vardist-/err3) 1.094 (13.59) 3.86 (1.921) 11.15 (1.184)
26 Non-planar-DNA 3-way junction(3p-5d-15fixdist/err0) 0.85 (0.019) 0.59 (0.041) 0.71 (0.027)
27 Non-planar-DNA 3-way junction(3p-5d-15vardist/err0) 0.110 (12.45) 5.26 (0.239) 12.34 (0.137)
28 Non-planar-DNA 3-way junction(3p-5d-15vardist/err3) 0.595 (12.20) 1.39 (1.337) 7.70 (1.083)
29 Non-planar-DNA 3-way junction(3p-5d-15vardist+/err3) 0.823 (11.98) 0.57 (1.863) 2.94 (0.890)
30 Non-planar-DNA 3-way junction(3p-5d-15vardist-/err3) 0.449 (13.33) 3.35 (1.793) 3.96 (0.893)