All issues

Search results

Support for non-canonical residues (TPO) in protein mutations: failure when attempting TPO → THR mutation with Perses.

Status: Open.

#1251 In choderalab/perses;

· vedantg-1311 opened on Apr 9, 2026

Issue in running protein mutation HTF setup with ATP cofactor

Status: Open.

#1250 In choderalab/perses;

· sukritsingh opened on Jun 4, 2025

OpenEye dependencies are a barrier to using perses

Status: Open.

#1248 In choderalab/perses;

· danielguion opened on Nov 21, 2024

IndexError with _vacdg_history if there is no vacuum trajectory

Status: Open.

#1247 In choderalab/perses;

· slochower opened on Apr 13, 2024

Improved reporting and state detection when passing tautomers as old_residue

Status: Open.

#1246 In choderalab/perses;

· sukritsingh opened on Apr 5, 2024

Update README?

documentation 📑Documentation enhancementsDocumentation enhancements

Status: Open.

#1244 In choderalab/perses;

· zhang-ivy opened on Dec 7, 2023

Allow specification of mapping dictionary in the pipeline

enhancement ✨

Status: Open.

#1241 In choderalab/perses;

· ijpulidos opened on Nov 6, 2023

·  

0.11.0: New top-level API

Allow user to specify list of atom indices to override default behavior for selecting the REST region

Status: Open.

#1226 In choderalab/perses;

· zhang-ivy opened on Aug 9, 2023

Fix potential bug in counterion implementation: get_water_indices()

Status: Open.

#1225 In choderalab/perses;

· zhang-ivy opened on Aug 9, 2023

Protein mutation protocol for alchemiscale

effort: medium

future

priority: mediumpriority mediumpriority medium

Status: Open.

#1222 In choderalab/perses;

· ijpulidos opened on Aug 1, 2023

·  

0.11.0: New top-level API

Migrate from PDB to PDBx/mmcif

enhancement ✨

Status: Open.

#1221 In choderalab/perses;

· ijpulidos opened on Jul 31, 2023

·  

0.11.0: New top-level API

Duplicate instances of self._setup_complex_phase() in relative_setup.py

priority: lowlow prioritylow priority

Status: Open.

#1219 In choderalab/perses;

· zhang-ivy opened on Jul 28, 2023