Added residue replacement to handle protein chemical modifications and NCAAs - #128
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gfzhou wants to merge 2 commits into
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Added residue replacement to handle protein chemical modifications and NCAAs#128gfzhou wants to merge 2 commits into
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r-krishna
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Jul 11, 2024
r-krishna
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needs some clarification in the README
| 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, |
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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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