Enzyme Design Tutorial

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

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"
+    }
+}

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)

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",