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Update examples.md
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mgiulini authored Apr 18, 2024
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Expand Up @@ -75,10 +75,12 @@ arctic3d --input_pdb example/1ppe_E.pdb --interface_file example/1ppe_E_example_
One may want to run ARCTIC3D on a custom pdb, without providing an interface file. Here the program extracts the pdb sequence and finds the corresponding uniprot ID. The input file is then renumbered according to the canonical numbering. Finally, the workflow showcased in [standard-uniprot-input](standard-uniprot-input) can be executed.

If known, the uniprot ID of the protein can be specified as follows:

```bash
arctic3d --input_pdb example/1ppe_E.pdb --input_uniprot P00760
```
On the one hand this allows to speed-up the execution by eliminating the need for the BLAST search. On the other hand, it allows to specify a uniprot ID different from the best-matching one (particularly useful if close homologues can be identified).

On the one hand this speeds up the execution by eliminating the need for the BLAST search. On the other hand, it allows to specify a uniprot ID different from the best-matching one (particularly useful if close homologues can be identified).

## uniprot-full-input

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