Chai-1 supports specifying covalent bonds as input, which specify covalent linkages between atoms in the folded complex. This is useful for specifying covalent modifications such as glycosylation events, but can be generally used to specify arbitrary "non-canonical" bonds in a structure; we demonstrate both cases below.
A few notes:
- Chai-1 was not trained on intra-chain bonds (e.g., disulfides), and we have not evaluated whether specifying such bond information yields expected behaviors.
- These bond restraints should not be used to specify modified amino acids that already have an associated CCD code; for these examples, include the modified residue's CCD code in parentheses directly in the sequence in place of its canonical residue, e.g.,
RKDES(MSE)EESto specify a selenomethionine at the 6th position.
We adopt an abbreviated syntax for specifying glycans, which is best explained with a series of examples.
Let's say we have a glycan that is a single sugar ring, a 2-acetamido-2-deoxy-beta-D-glucopyranose. The CCD code for this sugar is NAG, so we simply specify this sugar with the following fasta entry:
>protein|example-protein
...N...
>glycan|example-single-sugar
NAG
Now, a glycan is also covalently bound to a residue; to specify this, we include the following line in our restraints file (see our documentation on restraints as well):
| chainA | res_idxA | chainB | res_idxB | connection_type | confidence | min_distance_angstrom | max_distance_angstrom | comment | restraint_id |
|---|---|---|---|---|---|---|---|---|---|
| A | N436@N | B | @C1 | covalent | 1.0 | 0.0 | 0.0 | protein-glycan | bond1 |
Breaking this down, this specifies that the within chain A (the first entry in the fasta), the "N" residue at the 436-th position (1-indexed) as indicated by the "N436" prefix is bound, via its nitrogen "N" atom as indicated by the "@N" suffix, to the C1 atom in the first glycan ("@C1"). Ring numbering follows standard glycan ring number schemas. For other ligands, you will need check how the specific version of rdkit that we use in chai-lab (run uv pip list | grep rdkit for version) assigns atom names and use the same atom names to specify your bonds. In addition, note that the min and max distance fields are ignored, as is the confidence field.
Working through a more complex example, let's say we have a two-ring ligand such as that shown in the PDB structure 1AC5. We introduce syntax for specifying bonds within glycans within the fasta record as such:
>protein|example-protein
...N...
>glycan|example-dual-sugar
NAG(4-1 NAG)
This syntax specifies that the root of the glycan is the leading NAG ring. The parentheses indicate that we are attaching another molecule to the ring directly preceding the parentheses. The 4-1 syntax "draws" a bond between the O4 atom of the previous "root" NAG and the C1 atom of the subsequent NAG ring. Note that this syntax, when read left-to-right, is "building out" the glycan from the root sugar outwards.
To specify how this glycan ought to be connected to the protein, we again use the restraints file to specify a residue and atom to which the glycan is bound, and the carbon atom within the root glycan ring that is bound.
| chainA | res_idxA | chainB | res_idxB | connection_type | confidence | min_distance_angstrom | max_distance_angstrom | comment | restraint_id |
|---|---|---|---|---|---|---|---|---|---|
| A | N436@N | B | @C1 | covalent | 1.0 | 0.0 | 0.0 | protein-glycan | bond1 |
You can chain this syntax to create longer ligands:
>glycan|4-NAG-in-a-linear-chain
NAG(4-1 NAG(4-1 NAG(4-1 NAG)))
...and to create branched ligands
>glycan|branched-glycan
NAG(4-1 NAG(4-1 BMA(3-1 MAN)(6-1 MAN)))
This branched example has a root NAG ring followed by a NAG and a BMA, which then branches to two MAN rings. For additional examples of this syntax, please refer to the examples in tests/test_glycans.py.
We have included an example of how glycans can be specified under predict_glycosylated.py in this directory, along with its corresponding bonds.restraints csv file. This example is based on the PDB structure 1AC5. The predicted structrue (colored, glycans in purple and orange, protein in green) from this script should look like the following when aligned with the ground truth 1AC5 structure (gray):
You can also use covalent bonds to "connect" residues to non-glycan ligands. To demonstrate this, we use a single subunit from the homodimer 8CYO. We specify a fasta file with a protein sequence and SMILES string in 8cyo.fasta (we use SMILES for demonstration purposes even though this specific ligand has a CCD code) and the corresponding restraints in 8cyo.restraints. Folding this example with predict_covalent_ligand.py yields the following structure (RCSB ground truth structure shown in gray).
One might notice that in the above example, we are specifying CCD codes for sugar rings and connecting them to each other and an amino acid residue via various bonds. A subtle point is that the reference conformer for these sugar rings include OH hydroxyl groups that leave when bonds are formed. Under the hood, Chai-1 tries to automatically find and remove these atoms (see AllAtomStructureContext.drop_glycan_leaving_atoms_inplace for implementation), but this logic only drops leaving hydroxyl groups within glycan sugar rings. For other, non-sugar covalently attached ligands, please specify a SMILES string without the leaving atoms. If this does not work for your use case, please open a GitHub issue.