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Enzyme Design Tutorial (#210)

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* Docs: Installation FAQ space and minor RFD3 docs updates

Installation FAQ: created a document to specify any common installation issues and questions. Should be continuously updated based on logged issues and questions. Not specific to any model.

RFD3:
- changed the checkpoint files specified in the examples to rfd3_latest.ckpt
- updated information in input.md to clarify information based on recent issues that had been submitted

* Docs: Symlinks for RF3 and MPNN docs, RFD3 README minor edits

RF3 and MPNN: folders, index files, and symlinks were created in order to provide space for eventual RF3 and MPNN docs.

Several small changes in the RFD3 README to improve readability and  add a pointer to the PPI tutorial as a starting point for someone new to RFdiffusion tools.

* First draft of enzyme design tutorial. Minor typo fixes in other documents.

* First draft of nucleic acid binder tutorial, minor edits to the other tutorials

* Completed enzyme design tutorial, removal of NA binder tutorial from index

Made changes based on edits from Saman, added images, and created zip file containing sample outputs for an enzyme design tutorial.

I am waiting on edits for the NA binder design tutorial, so for now I have removed it from the documentation index.

* Removing file related to in-progress NA binder tutorial

* Removing file related to in-progress NA binder tutorial

* Final version of the enzyme design tutorial

Made small edits, created example files.

* Resolving merge conflicts
This commit is contained in:
Rachel Clune
2026-02-25 16:13:05 -08:00
committed by GitHub
parent 9f609e8758
commit 99a0cb773a
6 changed files with 121 additions and 5 deletions
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92
models/rfd3/docs/enzyme_tutorial_files/1euv_lig.pdb Normal file
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@@ -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

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models/rfd3/docs/enzyme_tutorial_files/rfd3_enzyme_tutorial.json Normal file
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{
"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"
}
}

8
models/rfd3/docs/tutorials/enzyme_design_tutorial.md
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@@ -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)

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models/rfd3/docs/tutorials/enzyme_tutorial_files/rfd3_enzyme_tutorial.json
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{
"1euv": {
"cys_1euv_lig": {
"input": "./1euv_lig.pdb",
"ligand": "l:g",
"unindex": "A514,A531,A574,A579-581",