Comments (3)
pgrinaway
commented on June 19, 2024
Ok, after a chat with @jchodera, we'll keep the above list except:
- Basic API test framework
- Finish relevant GeometryEngine stuff.
- Fix the TopologyProposalEngine to correctly deal with multiple possible alignments.
- Write a SAMSSampler, ExpandedEnsembleSampler, and adaptive bias SAMSSampler
- Include examples (host/guest, T4 Lysozyme)
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jchodera
commented on June 19, 2024
Sounds great. We should include another example that tests @juliebehr's MutationEngine too. There are mutations of T4 lysozyme that modulate the ligand affinities: L99A binders, L99A nonbinders, L99A/M102Q binders, L99A/M102Q non-binders, and a number of additional mutants in this paper.
from perses.
pgrinaway
commented on June 19, 2024
Going to close this, since this is mostly done.
from perses.
Related Issues (20)
- Integrate new atom mappers HOT 7
- Write initial initial and final structures in subdir
- AtomMapper fails when scaffolds have radicals HOT 1
- Creating legacy 0.10.x branch for longer term support -- main branch will become `gufe` refactor HOT 1
- Make sure we merge latest 0.10 branch before working on 0.11 refactor
- perses with mpi HOT 1
- Duplicate instances of `self._setup_complex_phase()` in relative_setup.py HOT 2
- Make `offline-freq` be the same as `checkpoint_interval` by default HOT 1
- Migrate from PDB to PDBx/mmcif HOT 1
- Protein mutation protocol for alchemiscale HOT 1
- Adapt MPi example with perses at least for protein mutation HOT 1
- Fix potential bug in counterion implementation: get_water_indices()
- Allow user to specify list of atom indices to override default behavior for selecting the REST region
- Support for use of custom force fields (e.g., one generated from openff-bespokefit) HOT 5
- Error with spectator ligands HOT 8
- Allow specification of mapping dictionary in the pipeline
- Update README? HOT 1
- Retrieving exact topology used for an endpoint in a relative transformation HOT 11
- Improved reporting and state detection when passing tautomers as `old_residue`
- IndexError with `_vacdg_history` if there is no vacuum trajectory HOT 3
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