Added residue replacement to handle protein chemical modifications and NCAAs #128
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r-krishna
requested changes
Jul 11, 2024
| residue_index_to_replace: 57 | ||
| input: examples/residue_replacement/SEP_ideal_trim.sdf | ||
| input_type: "sdf" | ||
| N_index_atom: 1 |
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is this 0 indexed or 1 indexed?
| C_index_atom = int(residue_replacement[chain].C_index_atom) | ||
| residues_to_atomize.append(AtomizedResidue( | ||
| chain, | ||
| 0, |
| @@ -263,6 +263,37 @@ becomes this so it can be parsed correctly: | |||
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| We know this syntax is hard to work with and we are happy to review PRs if anyone in the community can figure out how to specify all the necessary requirements in a more user friendly way! | |||
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| <a id="residue_replacement"></a> | |||
| ### Predicting Proteins with Chemical Modifications or Non-Canonical Amino Acids | |||
| To predict proteins with chemically modified residues or non-canonical amino acids, you can use residue replacement. This involves replacing the chemically modified residue or NCAA with a small molecule file that defines the structure of the modified residue. Here is an example of predicting a phosphorylated protein structure. (from `rf2aa/config/inference/residue_replacement.yaml`) | |||
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are there any edge cases with running these with protein multimers or cases with small molecules? does order of inputs matter?
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