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Initial commit of step-by-step instructions
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Brian D. Weitzner committed Oct 18, 2019
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3 changes: 3 additions & 0 deletions NOTES.txt
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Follow steps 1-4 to recapitulate the workflow from generated networks to matching in scaffolds. See NOES.txt in each subdirectory for instructions.

HBNetGen executable available upon request.
81 changes: 81 additions & 0 deletions step1_generate_network_stubs/MTK_RR_003.pdb
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HETATM 1 CE MTK X 1 -17.440 20.217 -11.921 1.00 20.00 C
HETATM 2 NZ MTK X 1 -18.747 20.428 -12.545 1.00 20.00 N
HETATM 3 C1 MTK X 1 -22.978 15.905 -5.636 1.00 20.00 C
HETATM 4 O1 MTK X 1 -23.208 15.285 -4.432 1.00 20.00 O
HETATM 5 C2 MTK X 1 -23.850 15.704 -6.700 1.00 20.00 C
HETATM 6 O2 MTK X 1 -22.078 19.625 -11.518 1.00 20.00 O
HETATM 7 C3 MTK X 1 -23.647 16.317 -7.900 1.00 20.00 C
HETATM 8 O3 MTK X 1 -20.599 19.496 -13.693 1.00 20.00 O
HETATM 9 C4 MTK X 1 -21.891 16.722 -5.799 1.00 20.00 C
HETATM 10 C5 MTK X 1 -21.644 17.370 -7.030 1.00 20.00 C
HETATM 11 C6 MTK X 1 -22.537 17.166 -8.107 1.00 20.00 C
HETATM 12 C7 MTK X 1 -22.284 17.814 -9.339 1.00 20.00 C
HETATM 13 C8 MTK X 1 -21.193 18.630 -9.513 1.00 20.00 C
HETATM 14 C9 MTK X 1 -20.872 19.341 -10.816 1.00 20.00 C
HETATM 15 C10 MTK X 1 -19.908 18.542 -11.694 1.00 20.00 C
HETATM 16 C11 MTK X 1 -19.502 19.277 -12.975 1.00 20.00 C
HETATM 17 C12 MTK X 1 -18.564 18.403 -13.785 1.00 20.00 C
HETATM 18 C13 MTK X 1 -20.333 18.820 -8.439 1.00 20.00 C
HETATM 19 C14 MTK X 1 -20.535 18.220 -7.234 1.00 20.00 C
HETATM 20 C15 MTK X 1 -24.336 14.430 -4.251 1.00 20.00 C
HETATM 21 H MTK X 1 -24.710 15.051 -6.598 1.00 20.00 H
HETATM 22 1HE MTK X 1 -16.821 19.563 -12.531 1.00 20.00 H
HETATM 23 2HE MTK X 1 -17.545 19.764 -10.937 1.00 20.00 H
HETATM 24 3HE MTK X 1 -16.915 21.163 -11.802 1.00 20.00 H
HETATM 25 2HZ MTK X 1 -19.323 20.929 -11.870 1.00 20.00 H
HETATM 26 H1 MTK X 1 -24.349 16.149 -8.710 1.00 20.00 H
HETATM 27 H2 MTK X 1 -21.209 16.875 -4.969 1.00 20.00 H
HETATM 28 H3 MTK X 1 -22.980 17.648 -10.153 1.00 20.00 H
HETATM 29 H4 MTK X 1 -22.629 18.806 -11.574 1.00 20.00 H
HETATM 30 H5 MTK X 1 -20.394 20.302 -10.569 1.00 20.00 H
HETATM 31 H6 MTK X 1 -20.349 17.572 -11.955 1.00 20.00 H
HETATM 32 H7 MTK X 1 -19.006 18.338 -11.104 1.00 20.00 H
HETATM 33 H8 MTK X 1 -18.090 18.984 -14.574 1.00 20.00 H
HETATM 34 H9 MTK X 1 -17.779 17.990 -13.156 1.00 20.00 H
HETATM 35 H10 MTK X 1 -19.082 17.570 -14.251 1.00 20.00 H
HETATM 36 H11 MTK X 1 -19.472 19.468 -8.565 1.00 20.00 H
HETATM 37 H12 MTK X 1 -19.837 18.396 -6.422 1.00 20.00 H
HETATM 38 H13 MTK X 1 -24.353 14.023 -3.242 1.00 20.00 H
HETATM 39 H14 MTK X 1 -25.263 14.977 -4.410 1.00 20.00 H
HETATM 40 H15 MTK X 1 -24.307 13.599 -4.952 1.00 20.00 H
CONECT 1 2 22 23 24
CONECT 2 1 16 25
CONECT 3 4 5 9
CONECT 4 3 20
CONECT 5 3 7 21
CONECT 6 14 29
CONECT 7 5 11 26
CONECT 8 16
CONECT 9 3 10 27
CONECT 10 9 11 19
CONECT 11 7 10 12
CONECT 12 11 13 28
CONECT 13 12 14 18
CONECT 14 6 13 15 30
CONECT 15 14 16 31 32
CONECT 16 2 8 15 17
CONECT 17 16 33 34 35
CONECT 18 13 19 36
CONECT 19 10 18 37
CONECT 20 4 38 39 40
CONECT 21 5
CONECT 22 1
CONECT 23 1
CONECT 24 1
CONECT 25 2
CONECT 26 7
CONECT 27 9
CONECT 28 12
CONECT 29 6
CONECT 30 14
CONECT 31 15
CONECT 32 15
CONECT 33 17
CONECT 34 17
CONECT 35 17
CONECT 36 18
CONECT 37 19
CONECT 38 20
CONECT 39 20
CONECT 40 20
END
81 changes: 81 additions & 0 deletions step1_generate_network_stubs/MTK_RR_003/MTK_RR_003.pdb
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HETATM 1 CE MTK X 1 -17.440 20.217 -11.921 1.00 20.00 C
HETATM 2 NZ MTK X 1 -18.747 20.428 -12.545 1.00 20.00 N
HETATM 3 C1 MTK X 1 -22.978 15.905 -5.636 1.00 20.00 C
HETATM 4 O1 MTK X 1 -23.208 15.285 -4.432 1.00 20.00 O
HETATM 5 C2 MTK X 1 -23.850 15.704 -6.700 1.00 20.00 C
HETATM 6 O2 MTK X 1 -22.078 19.625 -11.518 1.00 20.00 O
HETATM 7 C3 MTK X 1 -23.647 16.317 -7.900 1.00 20.00 C
HETATM 8 O3 MTK X 1 -20.599 19.496 -13.693 1.00 20.00 O
HETATM 9 C4 MTK X 1 -21.891 16.722 -5.799 1.00 20.00 C
HETATM 10 C5 MTK X 1 -21.644 17.370 -7.030 1.00 20.00 C
HETATM 11 C6 MTK X 1 -22.537 17.166 -8.107 1.00 20.00 C
HETATM 12 C7 MTK X 1 -22.284 17.814 -9.339 1.00 20.00 C
HETATM 13 C8 MTK X 1 -21.193 18.630 -9.513 1.00 20.00 C
HETATM 14 C9 MTK X 1 -20.872 19.341 -10.816 1.00 20.00 C
HETATM 15 C10 MTK X 1 -19.908 18.542 -11.694 1.00 20.00 C
HETATM 16 C11 MTK X 1 -19.502 19.277 -12.975 1.00 20.00 C
HETATM 17 C12 MTK X 1 -18.564 18.403 -13.785 1.00 20.00 C
HETATM 18 C13 MTK X 1 -20.333 18.820 -8.439 1.00 20.00 C
HETATM 19 C14 MTK X 1 -20.535 18.220 -7.234 1.00 20.00 C
HETATM 20 C15 MTK X 1 -24.336 14.430 -4.251 1.00 20.00 C
HETATM 21 H MTK X 1 -24.710 15.051 -6.598 1.00 20.00 H
HETATM 22 1HE MTK X 1 -16.821 19.563 -12.531 1.00 20.00 H
HETATM 23 2HE MTK X 1 -17.545 19.764 -10.937 1.00 20.00 H
HETATM 24 3HE MTK X 1 -16.915 21.163 -11.802 1.00 20.00 H
HETATM 25 2HZ MTK X 1 -19.323 20.929 -11.870 1.00 20.00 H
HETATM 26 H1 MTK X 1 -24.349 16.149 -8.710 1.00 20.00 H
HETATM 27 H2 MTK X 1 -21.209 16.875 -4.969 1.00 20.00 H
HETATM 28 H3 MTK X 1 -22.980 17.648 -10.153 1.00 20.00 H
HETATM 29 H4 MTK X 1 -22.629 18.806 -11.574 1.00 20.00 H
HETATM 30 H5 MTK X 1 -20.394 20.302 -10.569 1.00 20.00 H
HETATM 31 H6 MTK X 1 -20.349 17.572 -11.955 1.00 20.00 H
HETATM 32 H7 MTK X 1 -19.006 18.338 -11.104 1.00 20.00 H
HETATM 33 H8 MTK X 1 -18.090 18.984 -14.574 1.00 20.00 H
HETATM 34 H9 MTK X 1 -17.779 17.990 -13.156 1.00 20.00 H
HETATM 35 H10 MTK X 1 -19.082 17.570 -14.251 1.00 20.00 H
HETATM 36 H11 MTK X 1 -19.472 19.468 -8.565 1.00 20.00 H
HETATM 37 H12 MTK X 1 -19.837 18.396 -6.422 1.00 20.00 H
HETATM 38 H13 MTK X 1 -24.353 14.023 -3.242 1.00 20.00 H
HETATM 39 H14 MTK X 1 -25.263 14.977 -4.410 1.00 20.00 H
HETATM 40 H15 MTK X 1 -24.307 13.599 -4.952 1.00 20.00 H
CONECT 1 2 22 23 24
CONECT 2 1 16 25
CONECT 3 4 5 9
CONECT 4 3 20
CONECT 5 3 7 21
CONECT 6 14 29
CONECT 7 5 11 26
CONECT 8 16
CONECT 9 3 10 27
CONECT 10 9 11 19
CONECT 11 7 10 12
CONECT 12 11 13 28
CONECT 13 12 14 18
CONECT 14 6 13 15 30
CONECT 15 14 16 31 32
CONECT 16 2 8 15 17
CONECT 17 16 33 34 35
CONECT 18 13 19 36
CONECT 19 10 18 37
CONECT 20 4 38 39 40
CONECT 21 5
CONECT 22 1
CONECT 23 1
CONECT 24 1
CONECT 25 2
CONECT 26 7
CONECT 27 9
CONECT 28 12
CONECT 29 6
CONECT 30 14
CONECT 31 15
CONECT 32 15
CONECT 33 17
CONECT 34 17
CONECT 35 17
CONECT 36 18
CONECT 37 19
CONECT 38 20
CONECT 39 20
CONECT 40 20
END
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