Published January 2, 2018
| Version 0.20.0
Software
Open
choderalab/yank: 0.20.0 - Support for processing proteins through PDBFixer
Creators
- 1. @choderalab
- 2. Memorial Sloan Kettering Cancer Center
Description
- Adds an optional
pdbfixerdirective to themoleculessection of the YAML file through PDBFixer, a simple OpenMM-based protein structure processing tool. - The following options are accessible through the
pdbfixerdirective.replace_nonstandard_residues: Replace nonstandard amino acids.remove_heterogens: Remove heterogens (such as ligands and waters).add_missing_residues: Add missing residues from the SEQRES block.add_missing_atoms: Add missing heavy atoms.apply_mutations: Specify protein mutations (e.g., T315I).
Files
choderalab/yank-0.20.0.zip
Files
(8.3 MB)
| Name | Size | Download all |
|---|---|---|
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md5:57b6f089baecf305cd62395e7205c7a6
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8.3 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/choderalab/yank/tree/0.20.0 (URL)