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brianjimenez committed Nov 11, 2024
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1,050 changes: 1,050 additions & 0 deletions workshops/talca24/docking_challenge/data/6i2g.pdb
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932 changes: 932 additions & 0 deletions workshops/talca24/docking_challenge/data/6i2g_nanobody.pdb
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119 changes: 119 additions & 0 deletions workshops/talca24/docking_challenge/data/6i2g_peptide.pdb
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ATOM 962 N SER B 2 -7.389 23.006 -4.391 1.00 9.91 N
ATOM 963 CA SER B 2 -8.598 23.169 -5.140 1.00 9.83 C
ATOM 964 C SER B 2 -9.782 23.336 -4.176 1.00 8.99 C
ATOM 965 O SER B 2 -9.648 23.046 -2.969 1.00 9.82 O
ATOM 966 CB SER B 2 -8.753 21.965 -6.044 1.00 10.84 C
ATOM 967 OG SER B 2 -8.997 20.781 -5.268 1.00 9.27 O
ATOM 968 N ARG B 3 -10.929 23.668 -4.735 1.00 9.32 N
ATOM 969 CA ARG B 3 -12.226 23.689 -4.024 1.00 8.71 C
ATOM 970 C ARG B 3 -12.470 22.345 -3.332 1.00 8.52 C
ATOM 971 O ARG B 3 -12.764 22.358 -2.127 1.00 8.71 O
ATOM 972 CB ARG B 3 -13.303 24.055 -5.027 1.00 8.83 C
ATOM 973 CG ARG B 3 -14.701 23.806 -4.494 1.00 9.36 C
ATOM 974 CD ARG B 3 -15.752 24.570 -5.262 1.00 9.82 C
ATOM 975 NE ARG B 3 -17.084 24.046 -5.126 1.00 11.13 N
ATOM 976 CZ ARG B 3 -17.956 24.320 -4.159 1.00 9.72 C
ATOM 977 NH1 ARG B 3 -19.158 23.756 -4.195 1.00 10.74 N
ATOM 978 NH2 ARG B 3 -17.623 25.120 -3.154 1.00 9.78 N
ATOM 979 N LEU B 4 -12.329 21.218 -4.051 1.00 8.48 N
ATOM 980 CA LEU B 4 -12.569 19.917 -3.407 1.00 7.84 C
ATOM 981 C LEU B 4 -11.552 19.761 -2.286 1.00 6.86 C
ATOM 982 O LEU B 4 -11.868 19.198 -1.268 1.00 7.15 O
ATOM 983 CB LEU B 4 -12.505 18.770 -4.423 1.00 7.86 C
ATOM 984 CG LEU B 4 -13.793 18.635 -5.216 1.00 7.86 C
ATOM 985 CD1 LEU B 4 -13.595 17.878 -6.508 1.00 8.10 C
ATOM 986 CD2 LEU B 4 -14.893 17.971 -4.377 1.00 8.15 C
ATOM 987 N GLU B 5 -10.284 20.088 -2.514 1.00 7.15 N
ATOM 988 CA GLU B 5 -9.288 19.832 -1.482 1.00 7.49 C
ATOM 989 C GLU B 5 -9.523 20.692 -0.230 1.00 7.24 C
ATOM 990 O GLU B 5 -9.267 20.162 0.879 1.00 7.30 O
ATOM 991 CB GLU B 5 -7.913 20.066 -2.085 1.00 7.81 C
ATOM 992 CG GLU B 5 -7.497 18.949 -3.033 1.00 8.33 C
ATOM 993 CD GLU B 5 -6.201 19.238 -3.772 1.00 10.27 C
ATOM 994 OE1 GLU B 5 -5.804 20.429 -3.875 1.00 12.06 O
ATOM 995 OE2 GLU B 5 -5.640 18.271 -4.368 1.00 10.74 O
ATOM 996 N GLU B 6 -10.041 21.906 -0.389 1.00 7.76 N
ATOM 997 CA GLU B 6 -10.387 22.746 0.791 1.00 8.38 C
ATOM 998 C GLU B 6 -11.566 22.114 1.537 1.00 7.81 C
ATOM 999 O GLU B 6 -11.544 22.095 2.736 1.00 8.68 O
ATOM 1000 CB GLU B 6 -10.687 24.150 0.305 1.00 9.14 C
ATOM 1001 CG GLU B 6 -9.401 24.809 -0.172 1.00 9.97 C
ATOM 1002 CD GLU B 6 -9.634 26.157 -0.784 1.00 12.07 C
ATOM 1003 OE1 GLU B 6 -10.750 26.356 -1.339 1.00 14.17 O
ATOM 1004 OE2 GLU B 6 -8.702 27.014 -0.709 1.00 11.77 O
ATOM 1005 N GLU B 7 -12.525 21.543 0.813 1.00 8.18 N
ATOM 1006 CA GLU B 7 -13.699 20.875 1.438 1.00 8.01 C
ATOM 1007 C GLU B 7 -13.243 19.572 2.115 1.00 7.44 C
ATOM 1008 O GLU B 7 -13.635 19.277 3.225 1.00 8.05 O
ATOM 1009 CB GLU B 7 -14.773 20.669 0.381 1.00 8.52 C
ATOM 1010 CG GLU B 7 -16.014 19.938 0.873 1.00 9.58 C
ATOM 1011 CD GLU B 7 -16.803 20.616 1.973 1.00 11.13 C
ATOM 1012 OE1 GLU B 7 -16.550 21.799 2.274 1.00 10.50 O
ATOM 1013 OE2 GLU B 7 -17.624 19.882 2.622 1.00 12.31 O
ATOM 1014 N LEU B 8 -12.356 18.798 1.486 1.00 6.97 N
ATOM 1015 CA LEU B 8 -11.787 17.584 2.104 1.00 7.16 C
ATOM 1016 C LEU B 8 -11.058 17.937 3.419 1.00 7.36 C
ATOM 1017 O LEU B 8 -11.185 17.201 4.422 1.00 8.05 O
ATOM 1018 CB LEU B 8 -10.799 16.925 1.122 1.00 7.51 C
ATOM 1019 CG LEU B 8 -11.412 16.216 -0.079 1.00 7.93 C
ATOM 1020 CD1 LEU B 8 -10.327 15.647 -0.983 1.00 7.31 C
ATOM 1021 CD2 LEU B 8 -12.345 15.113 0.379 1.00 7.93 C
ATOM 1022 N ARG B 9 -10.242 19.014 3.436 1.00 7.45 N
ATOM 1023 CA ARG B 9 -9.527 19.407 4.670 1.00 8.89 C
ATOM 1024 C ARG B 9 -10.524 19.663 5.814 1.00 8.84 C
ATOM 1025 O ARG B 9 -10.211 19.276 6.962 1.00 10.70 O
ATOM 1026 CB ARG B 9 -8.636 20.615 4.414 1.00 9.71 C
ATOM 1027 CG ARG B 9 -7.726 20.929 5.599 1.00 10.35 C
ATOM 1028 CD ARG B 9 -7.879 22.358 6.086 1.00 12.24 C
ATOM 1029 NE ARG B 9 -9.112 22.587 6.839 1.00 12.42 N
ATOM 1030 CZ ARG B 9 -9.257 22.526 8.165 1.00 13.33 C
ATOM 1031 NH1 ARG B 9 -10.450 22.784 8.715 1.00 15.26 N
ATOM 1032 NH2 ARG B 9 -8.231 22.220 8.947 1.00 14.04 N
ATOM 1033 N ARG B 10 -11.626 20.331 5.518 1.00 9.25 N
ATOM 1034 CA ARG B 10 -12.672 20.632 6.516 1.00 9.93 C
ATOM 1035 C ARG B 10 -13.204 19.314 7.068 1.00 9.13 C
ATOM 1036 O ARG B 10 -13.240 19.125 8.290 1.00 9.62 O
ATOM 1037 CB ARG B 10 -13.788 21.442 5.858 1.00 11.91 C
ATOM 1038 CG ARG B 10 -14.821 21.982 6.839 1.00 14.09 C
ATOM 1039 CD ARG B 10 -16.016 22.617 6.151 1.00 16.74 C
ATOM 1040 NE ARG B 10 -16.851 21.675 5.408 1.00 19.09 N
ATOM 1041 CZ ARG B 10 -17.718 20.796 5.943 1.00 22.22 C
ATOM 1042 NH1 ARG B 10 -17.875 20.721 7.253 1.00 24.96 N
ATOM 1043 NH2 ARG B 10 -18.430 19.980 5.177 1.00 20.93 N
ATOM 1044 N ARG B 11 -13.593 18.396 6.174 1.00 8.22 N
ATOM 1045 CA ARG B 11 -14.171 17.109 6.607 1.00 8.01 C
ATOM 1046 C ARG B 11 -13.183 16.265 7.418 1.00 8.34 C
ATOM 1047 O ARG B 11 -13.628 15.498 8.326 1.00 9.36 O
ATOM 1048 CB ARG B 11 -14.692 16.367 5.383 1.00 7.59 C
ATOM 1049 CG ARG B 11 -15.880 17.063 4.724 1.00 7.50 C
ATOM 1050 CD ARG B 11 -16.300 16.443 3.425 1.00 7.56 C
ATOM 1051 NE ARG B 11 -17.446 17.139 2.846 1.00 7.47 N
ATOM 1052 CZ ARG B 11 -18.561 16.605 2.338 1.00 7.07 C
ATOM 1053 NH1 ARG B 11 -18.777 15.301 2.326 1.00 6.85 N
ATOM 1054 NH2 ARG B 11 -19.437 17.418 1.780 1.00 7.10 N
ATOM 1055 N LEU B 12 -11.891 16.263 7.060 1.00 8.34 N
ATOM 1056 CA LEU B 12 -10.864 15.428 7.716 1.00 8.74 C
ATOM 1057 C LEU B 12 -10.485 15.990 9.088 1.00 8.81 C
ATOM 1058 O LEU B 12 -9.863 15.214 9.851 1.00 10.29 O
ATOM 1059 CB LEU B 12 -9.619 15.346 6.837 1.00 8.43 C
ATOM 1060 CG LEU B 12 -9.815 14.557 5.540 1.00 7.87 C
ATOM 1061 CD1 LEU B 12 -8.728 14.861 4.547 1.00 7.49 C
ATOM 1062 CD2 LEU B 12 -9.888 13.076 5.848 1.00 8.35 C
ATOM 1063 N THR B 13 -10.927 17.193 9.443 1.00 10.15 N
ATOM 1064 CA THR B 13 -10.655 17.753 10.800 1.00 12.11 C
ATOM 1065 C THR B 13 -11.910 17.830 11.657 1.00 13.79 C
ATOM 1066 O THR B 13 -11.747 18.118 12.873 1.00 14.74 O
ATOM 1067 CB THR B 13 -9.979 19.115 10.658 1.00 15.29 C
ATOM 1068 OG1 THR B 13 -10.898 20.027 10.082 1.00 21.35 O
ATOM 1069 CG2 THR B 13 -8.766 19.063 9.776 1.00 16.91 C
ATOM 1070 N GLU B 14 -13.086 17.544 11.082 1.00 13.23 N
ATOM 1071 CA GLU B 14 -14.371 17.496 11.826 1.00 15.35 C
ATOM 1072 C GLU B 14 -14.204 16.376 12.846 1.00 15.78 C
ATOM 1073 O GLU B 14 -13.842 15.209 12.667 1.00 14.68 O
ATOM 1074 CB GLU B 14 -15.564 17.218 10.902 1.00 20.77 C
ATOM 1075 CG GLU B 14 -16.864 17.938 11.248 1.00 28.23 C
ATOM 1076 CD GLU B 14 -17.180 18.251 12.708 1.00 37.63 C
ATOM 1077 OE1 GLU B 14 -17.931 17.458 13.378 1.00 47.96 O
ATOM 1078 OE2 GLU B 14 -16.720 19.316 13.178 1.00 43.64 O
TER
END
68 changes: 68 additions & 0 deletions workshops/talca24/docking_challenge/data/talca_peptide.pdb
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ATOM 1 CG2 THR A 1 2.902 -2.045 2.374 1.00 0.00 C
ATOM 2 CB THR A 1 3.733 -1.412 1.286 1.00 0.00 C
ATOM 3 OG1 THR A 1 3.302 -1.694 0.004 1.00 0.00 O
ATOM 4 CA THR A 1 4.016 0.038 1.548 1.00 0.00 C
ATOM 5 N THR A 1 4.446 0.134 2.931 1.00 0.00 N
ATOM 6 C THR A 1 2.917 0.960 1.238 1.00 0.00 C
ATOM 7 O THR A 1 2.475 1.666 2.211 1.00 0.00 O
ATOM 8 HG21 THR A 1 3.043 -3.131 2.329 1.00 0.00 H
ATOM 9 HG22 THR A 1 1.843 -1.723 2.376 1.00 0.00 H
ATOM 10 HG23 THR A 1 3.319 -1.702 3.345 1.00 0.00 H
ATOM 11 HB THR A 1 4.738 -1.925 1.368 1.00 0.00 H
ATOM 12 HG1 THR A 1 2.380 -2.045 0.093 1.00 0.00 H
ATOM 13 HA THR A 1 4.885 0.329 0.921 1.00 0.00 H
ATOM 14 H2 THR A 1 3.975 0.879 3.463 1.00 0.00 H
ATOM 15 H3 THR A 1 5.463 0.109 3.064 1.00 0.00 H
ATOM 16 CB ALA A 2 1.690 3.273 -1.016 1.00 0.00 C
ATOM 17 CA ALA A 2 1.265 2.047 -0.227 1.00 0.00 C
ATOM 18 N ALA A 2 2.327 1.121 -0.026 1.00 0.00 N
ATOM 19 C ALA A 2 0.006 1.475 -0.756 1.00 0.00 C
ATOM 20 O ALA A 2 -0.946 2.306 -0.931 1.00 0.00 O
ATOM 21 HB1 ALA A 2 2.304 3.054 -1.893 1.00 0.00 H
ATOM 22 HB2 ALA A 2 0.765 3.831 -1.286 1.00 0.00 H
ATOM 23 HB3 ALA A 2 2.270 3.995 -0.387 1.00 0.00 H
ATOM 24 HA ALA A 2 1.005 2.477 0.787 1.00 0.00 H
ATOM 25 H ALA A 2 2.688 0.538 -0.838 1.00 0.00 H
ATOM 26 CD1 LEU A 3 -2.546 -1.611 -5.055 1.00 0.00 C
ATOM 27 CG LEU A 3 -2.732 -1.114 -3.619 1.00 0.00 C
ATOM 28 CD2 LEU A 3 -3.752 -0.020 -3.552 1.00 0.00 C
ATOM 29 CB LEU A 3 -1.418 -0.737 -3.007 1.00 0.00 C
ATOM 30 CA LEU A 3 -1.541 -0.226 -1.591 1.00 0.00 C
ATOM 31 N LEU A 3 -0.217 0.133 -1.072 1.00 0.00 N
ATOM 32 C LEU A 3 -2.112 -1.294 -0.745 1.00 0.00 C
ATOM 33 O LEU A 3 -3.281 -1.751 -0.870 1.00 0.00 O
ATOM 34 HD11 LEU A 3 -3.549 -1.789 -5.455 1.00 0.00 H
ATOM 35 HD12 LEU A 3 -1.916 -0.927 -5.647 1.00 0.00 H
ATOM 36 HD13 LEU A 3 -2.040 -2.593 -4.967 1.00 0.00 H
ATOM 37 HG LEU A 3 -3.132 -2.002 -3.087 1.00 0.00 H
ATOM 38 HD21 LEU A 3 -3.305 0.980 -3.365 1.00 0.00 H
ATOM 39 HD22 LEU A 3 -4.535 -0.301 -2.824 1.00 0.00 H
ATOM 40 HD23 LEU A 3 -4.299 0.007 -4.541 1.00 0.00 H
ATOM 41 HB2 LEU A 3 -0.824 -0.052 -3.649 1.00 0.00 H
ATOM 42 HB3 LEU A 3 -0.804 -1.688 -3.002 1.00 0.00 H
ATOM 43 HA LEU A 3 -2.198 0.662 -1.649 1.00 0.00 H
ATOM 44 H LEU A 3 0.544 -0.559 -0.936 1.00 0.00 H
ATOM 45 N CYS A 4 -1.347 -1.911 0.319 1.00 0.00 N
ATOM 46 CA CYS A 4 -1.970 -2.964 1.126 1.00 0.00 C
ATOM 47 CB CYS A 4 -1.323 -4.313 0.901 1.00 0.00 C
ATOM 48 SG CYS A 4 0.410 -4.250 1.337 1.00 0.00 S
ATOM 49 C CYS A 4 -1.914 -2.512 2.537 1.00 0.00 C
ATOM 50 O CYS A 4 -2.416 -3.304 3.402 1.00 0.00 O
ATOM 51 H CYS A 4 -0.378 -1.627 0.521 1.00 0.00 H
ATOM 52 HA CYS A 4 -3.034 -3.100 0.838 1.00 0.00 H
ATOM 53 HB2 CYS A 4 -1.450 -4.531 -0.174 1.00 0.00 H
ATOM 54 HB3 CYS A 4 -1.913 -5.042 1.451 1.00 0.00 H
ATOM 55 HG CYS A 4 1.169 -4.762 0.267 1.00 0.00 H
ATOM 56 CB ALA A 5 0.099 -0.839 4.814 1.00 0.00 C
ATOM 57 CA ALA A 5 -1.353 -0.960 4.344 1.00 0.00 C
ATOM 58 N ALA A 5 -1.341 -1.273 2.941 1.00 0.00 N
ATOM 59 C ALA A 5 -1.946 0.389 4.607 1.00 0.00 C
ATOM 60 O ALA A 5 -2.370 1.131 3.682 1.00 0.00 O
ATOM 61 OXT ALA A 5 -2.022 0.820 5.911 1.00 0.00 O
ATOM 62 HB1 ALA A 5 0.164 -0.571 5.877 1.00 0.00 H
ATOM 63 HB2 ALA A 5 0.521 -0.018 4.165 1.00 0.00 H
ATOM 64 HB3 ALA A 5 0.619 -1.757 4.541 1.00 0.00 H
ATOM 65 HA ALA A 5 -1.827 -1.758 4.916 1.00 0.00 H
ATOM 66 H ALA A 5 -0.934 -0.635 2.224 1.00 0.00 H
TER 67 ALA A 5
END
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18 changes: 7 additions & 11 deletions workshops/talca24/docking_challenge/index.md
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Expand Up @@ -31,33 +31,29 @@ With the aim of practicing and testing the ISM capabilities of the LightDock sof
### 2.1. The bread: 🍞

<p align="center">
<img src="docking_challenge/images/bread.png">
<img src="docking_challenge/images/6i2g_nanobody.png">
</p>

### 2.2. The stuffing: 🥩🥬🍅

<p align="center">
<img src="docking_challenge/images/stuffing.png">
<img src="docking_challenge/images/talca_peptide.gif">
</p>

### 2.3. The goal: 🌭

Is that a protein? Is that a star? No, it is the Turkish flag! 🇹🇷
Is that a <em>completo</em>? Is it <em>mojado</em>? Oh, wait, it is our ***completo molecular mojado***!

<p align="center">
<img src="docking_challenge/images/turkey_molecular_flag.gif">
<img src="docking_challenge/images/challenge.png">
</p>


## 3. Tips & tricks

1️⃣ Blind docking will probably not help a lot ([see a simulation](https://server.lightdock.org/job/run/d4431a1e054c43db83e1c2748b1f87a406dcec6f48d24bc3990fa650e607d843) we have prepared for you).
1️⃣ Blind docking will probably help since we are able to recover a similar interface ([see a simulation](https://server.lightdock.org/job/run/97308c2b7be4279d2283417e65ac5fde3761fb98fbc44b4087a8ebe5d1e112e7) we have prepared for you).

2️⃣ Docking simulations tend to maximize/minimize scoring functions by increasing the number of interactions. This usually favors larger binding interfaces, which is not the case for this challenge.
2️⃣ Docking simulations tend to maximize/minimize scoring functions by increasing the number of interactions. This usually favors larger binding interfaces, it might be the case for this challenge.

3️⃣ Residue restraints might definitely help to place our ligand in the good binding interface, but capturing this specific planar shape [is difficult](https://server.lightdock.org/job/run/8f6b5c739b6add17aa067a1a981395676a47650b928b454cb7daefe2cbce491e).

We have prepare two structures for you:

* <em>Bread</em> protein: [bread.pdb](docking_challenge/data/bread.pdb)
3️⃣ Residue restraints might definitely help to place our ligand in the good binding interface, but this is a totally new interaction compared to the native complex.

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