diff --git a/models/rfd3/docs/enzyme_tutorial_files/1euv_lig.pdb b/models/rfd3/docs/enzyme_tutorial_files/1euv_lig.pdb new file mode 100644 index 00000000..0fa5742b --- /dev/null +++ b/models/rfd3/docs/enzyme_tutorial_files/1euv_lig.pdb @@ -0,0 +1,92 @@ +ATOM 2 N HIS A 514 3.231 1.208 -1.240 1.00 19.42 A N +ATOM 3 CA HIS A 514 1.911 1.858 -1.146 1.00 18.23 A C +ATOM 4 C HIS A 514 1.410 2.170 -2.547 1.00 16.65 A C +ATOM 5 O HIS A 514 2.223 2.219 -3.470 1.00 18.87 A O +ATOM 6 CB HIS A 514 2.084 3.200 -0.401 1.00 18.92 A C +ATOM 7 CG HIS A 514 0.793 3.885 -0.097 1.00 19.11 A C +ATOM 8 CD2 HIS A 514 0.480 5.175 -0.343 1.00 19.33 A C +ATOM 9 ND1 HIS A 514 -0.281 3.307 0.570 1.00 19.64 A N +ATOM 10 CE1 HIS A 514 -1.232 4.247 0.679 1.00 20.67 A C +ATOM 11 NE2 HIS A 514 -0.784 5.363 0.136 1.00 18.73 A N +ATOM 12 N ASP A 531 -4.991 9.875 -2.283 1.00 18.01 A N +ATOM 13 CA ASP A 531 -4.198 8.868 -1.542 1.00 17.65 A C +ATOM 14 C ASP A 531 -5.028 8.515 -0.313 1.00 17.93 A C +ATOM 15 O ASP A 531 -5.344 9.384 0.513 1.00 19.21 A O +ATOM 16 CB ASP A 531 -2.843 9.512 -1.268 1.00 18.96 A C +ATOM 17 CG ASP A 531 -1.823 8.638 -0.562 1.00 19.66 A C +ATOM 18 OD1 ASP A 531 -2.229 7.763 0.218 1.00 20.25 A O +ATOM 19 OD2 ASP A 531 -0.605 8.900 -0.780 1.00 19.95 A O1- +ATOM 20 N GLN A 574 -7.907 4.613 4.461 1.00 20.37 A N +ATOM 21 CA GLN A 574 -7.953 3.179 4.855 1.00 21.00 A C +ATOM 22 C GLN A 574 -7.671 3.054 6.344 1.00 21.03 A C +ATOM 23 O GLN A 574 -6.759 3.718 6.872 1.00 20.78 A O +ATOM 24 CB GLN A 574 -6.902 2.474 3.981 1.00 21.23 A C +ATOM 25 CG GLN A 574 -5.460 2.863 4.335 1.00 22.92 A C +ATOM 26 CD GLN A 574 -4.523 2.355 3.261 1.00 23.64 A C +ATOM 27 NE2 GLN A 574 -3.727 1.344 3.595 1.00 24.35 A N +ATOM 28 OE1 GLN A 574 -4.554 2.817 2.125 1.00 23.51 A O +ATOM 29 N ASP A 579 -4.972 -2.251 2.419 1.00 16.24 A N +ATOM 30 CA ASP A 579 -6.009 -1.965 1.401 1.00 15.40 A C +ATOM 31 C ASP A 579 -5.673 -0.876 0.414 1.00 15.59 A C +ATOM 32 O ASP A 579 -6.577 -0.537 -0.384 1.00 16.28 A O +ATOM 33 CB ASP A 579 -7.339 -1.639 2.096 1.00 16.76 A C +ATOM 34 CG ASP A 579 -8.180 -2.869 2.367 1.00 18.53 A C +ATOM 35 OD1 ASP A 579 -8.022 -3.926 1.704 1.00 18.83 A O +ATOM 36 OD2 ASP A 579 -9.038 -2.793 3.279 1.00 20.44 A O1- +ATOM 37 N CYS A 580 -4.482 -0.303 0.456 1.00 14.58 A N +ATOM 38 CA CYS A 580 -4.229 0.856 -0.451 1.00 14.75 A C +ATOM 39 C CYS A 580 -4.592 0.525 -1.890 1.00 15.30 A C +ATOM 40 O CYS A 580 -5.133 1.439 -2.570 1.00 15.92 A O +ATOM 41 CB CYS A 580 -2.811 1.409 -0.381 1.00 16.92 A C +ATOM 42 SG CYS A 580 -1.587 0.078 -0.708 1.00 15.01 A S +ATOM 43 N GLY A 581 -4.214 -0.616 -2.427 1.00 15.26 A N +ATOM 44 CA GLY A 581 -4.496 -0.901 -3.873 1.00 15.15 A C +ATOM 45 C GLY A 581 -6.031 -0.979 -4.060 1.00 12.80 A C +ATOM 46 O GLY A 581 -6.496 -0.558 -5.161 1.00 16.14 A O +TER +HETATM 47 C2 l:g B 1 0.721 0.361 2.697 1.00 0.00 B C +HETATM 48 O3 l:g B 1 -2.014 -0.494 1.873 1.00 0.00 B O +HETATM 49 C4 l:g B 1 -0.420 -1.974 0.850 1.00 0.00 B C +HETATM 50 C5 l:g B 1 0.633 -2.135 -0.222 1.00 0.00 B C +HETATM 51 C8 l:g B 1 -0.950 -0.521 0.955 1.00 0.00 B C +HETATM 52 C12 l:g B 1 1.587 -0.654 3.148 1.00 0.00 B C +HETATM 53 C13 l:g B 1 2.184 -0.571 4.411 1.00 0.00 B C +HETATM 54 O14 l:g B 1 2.997 -1.544 4.811 1.00 0.00 B O +HETATM 55 C15 l:g B 1 3.599 -1.534 5.994 1.00 0.00 B C +HETATM 56 C16 l:g B 1 3.396 -0.477 6.884 1.00 0.00 B C +HETATM 57 C17 l:g B 1 2.549 0.578 6.518 1.00 0.00 B C +HETATM 58 C18 l:g B 1 1.924 0.537 5.251 1.00 0.00 B C +HETATM 59 C19 l:g B 1 1.061 1.550 4.794 1.00 0.00 B C +HETATM 60 C20 l:g B 1 2.333 1.717 7.480 1.00 0.00 B C +HETATM 61 O21 l:g B 1 4.358 -2.487 6.314 1.00 0.00 B O +HETATM 62 C22 l:g B 1 0.472 1.457 3.531 1.00 0.00 B C +HETATM 63 C23 l:g B 1 0.259 -2.375 -1.555 1.00 0.00 B C +HETATM 64 C24 l:g B 1 1.235 -2.502 -2.549 1.00 0.00 B C +HETATM 65 C25 l:g B 1 2.589 -2.391 -2.220 1.00 0.00 B C +HETATM 66 C26 l:g B 1 2.969 -2.152 -0.897 1.00 0.00 B C +HETATM 67 C27 l:g B 1 1.997 -2.024 0.100 1.00 0.00 B C +HETATM 68 O1 l:g B 1 0.085 0.352 1.440 1.00 0.00 B O +CONECT 42 51 +CONECT 47 52 62 68 +CONECT 48 51 +CONECT 49 50 51 +CONECT 50 49 63 67 +CONECT 51 42 48 49 68 +CONECT 52 47 53 +CONECT 53 52 54 58 +CONECT 54 53 55 +CONECT 55 54 56 61 +CONECT 56 55 57 +CONECT 57 56 58 60 +CONECT 58 53 57 59 +CONECT 59 58 62 +CONECT 60 57 +CONECT 61 55 +CONECT 62 47 59 +CONECT 63 50 64 +CONECT 64 63 65 +CONECT 65 64 66 +CONECT 66 65 67 +CONECT 67 50 66 +CONECT 68 47 51 +END diff --git a/models/rfd3/docs/enzyme_tutorial_files/outputs.zip b/models/rfd3/docs/enzyme_tutorial_files/outputs.zip new file mode 100644 index 00000000..60854a6a Binary files /dev/null and b/models/rfd3/docs/enzyme_tutorial_files/outputs.zip differ diff --git a/models/rfd3/docs/enzyme_tutorial_files/rfd3_enzyme_tutorial.json b/models/rfd3/docs/enzyme_tutorial_files/rfd3_enzyme_tutorial.json new file mode 100644 index 00000000..e567c5dc --- /dev/null +++ b/models/rfd3/docs/enzyme_tutorial_files/rfd3_enzyme_tutorial.json @@ -0,0 +1,24 @@ +{ + "1euv": { + "input": "./1euv_lig.pdb", + "ligand": "l:g", + "unindex": "A514,A531,A574,A579-581", + "length": "100-200", + "ori_token": [0, 1, 0], + "select_fixed_atoms": { + "A514":"NE2,CE1,ND1,CD2,CG,CB", + "A531":"OD1,CG,OD2,CB", + "A574":"NE2,CD,OE1,CG", + "A579":"C,O,CA,N", + "A580":"SG,CB,CA,N,C,O", + "A581":"C,O,CA,N" + }, + "select_buried": { + "l:g": "O1,C8,O3,C4,C5,C23,C24,C25,C26,C27" + }, + "select_exposed": { + "l:g": "C2,C22,C19,C18,C17,C20,C16,C15,O21,O14,C13,C12" + }, + "select_unfixed_sequence": "A579,A581" + } +} diff --git a/models/rfd3/docs/tutorials/enzyme_design_tutorial.md b/models/rfd3/docs/tutorials/enzyme_design_tutorial.md index f142b3dc..19d674d0 100644 --- a/models/rfd3/docs/tutorials/enzyme_design_tutorial.md +++ b/models/rfd3/docs/tutorials/enzyme_design_tutorial.md @@ -33,7 +33,7 @@ There is also a pre-made JSON file available in `foundry/models/rfd3/docs/enzyme (enzyme-creating-the-json-file)= ## Creating the JSON file -In the next few sections we will be briefly describing the settings we will be using for this example enzyme design project. If you would like more information about the options discussed here or information about the other options that are available, see the [input specification](input.md) documentation. +In the next few sections we will be briefly describing the settings we will be using for this example enzyme design project. If you would like more information about the options discussed here or information about the other options that are available, see the [input specification](../input.md) documentation. 1. Using your editor of choice, open a new file called `rfd3_enzyme_tutorial.json`. This is where we will be storing the options we will use to constrain our enzyme design. 1. This is a JSON file, so all of the options contained in it need to be encapsulated in curly braces ({}). Go ahead and add a pair of these to your file. @@ -55,7 +55,7 @@ In the next few sections we will be briefly describing the settings we will be u "ligand": "l:g", ``` ```{note} - The ligand used in this tutorial is not a real molecule. Placing a colon (:) in your ligand name ensures that it does not match a molecule in the [Chemical Component Database](https://www.wwpdb.org/data/ccd). If you are running a calculation that uses a real ligand, feel free to use its actual chemical identifier. + The ligand in this tutorial is a real molecule, but not one listed in the [Chemical Component Database](https://www.wwpdb.org/data/ccd) or the [RCSB Protein Data Bank](https://www.rcsb.org/). Placing a colon (:) in your ligand name ensures that it does not match a molecule in the Chemical Component Database. If you are running a calculation that uses a real ligand, feel free to use its actual chemical identifier. ``` 1. Add an option to `unindex` the residues in the input file. These residues were determined to be important for the enzymatic activity we are trying to create and design a protein around. However, we don't know where in our designed structure we want these enzymes to be, making this option incredibly useful for enzyme design: ```json @@ -168,10 +168,10 @@ You can see that the portion of the ligand that was specified as exposed (blue) ``` ## Conclusion -You have now set up an RFD3 calculation and successfully ran the inference code for an enzyme design problem. While the options discussed here are particularly useful in enzyme design projects, RFD3 has many more that you can explore by looking at (input.md). +You have now set up an RFD3 calculation and successfully ran the inference code for an enzyme design problem. While the options discussed here are particularly useful in enzyme design projects, RFD3 has many more that you can explore by looking at {doc}`../input`. (enzyme-references)= ## References and Further Reading -- For more information on the different inference settings in RFD3, see [input.md](../input.md) +- For more information on the different inference settings in RFD3, see {doc}`../input` - The calculation presented here was used to benchmark RFdiffusion2, for more information see [Atom-level enzyme active site scaffolding using RFdiffusion2](https://www.nature.com/articles/s41592-025-02975-x) - A more thorough discussion of the settings and configuration options in RFD3 can be found [here](../intro_inference_calculations.md) \ No newline at end of file diff --git a/models/rfd3/docs/tutorials/enzyme_tutorial_files/outputs.zip b/models/rfd3/docs/tutorials/enzyme_tutorial_files/outputs.zip index 1c4aa949..1ae0de01 100644 Binary files a/models/rfd3/docs/tutorials/enzyme_tutorial_files/outputs.zip and b/models/rfd3/docs/tutorials/enzyme_tutorial_files/outputs.zip differ diff --git a/models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json b/models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json index e567c5dc..da801154 100644 --- a/models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json +++ b/models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json @@ -1,5 +1,5 @@ { - "1euv": { + "cys_1euv_lig": { "input": "./1euv_lig.pdb", "ligand": "l:g", "unindex": "A514,A531,A574,A579-581",