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returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["expanded-ensembles","free-energy-perturbation","molecular-design","molecular-dynamics","openmm","python","relative-free-energy","simulation"],"created_at":"2025-10-21T19:06:51.554Z","updated_at":"2026-02-18T21:02:54.465Z","avatar_url":"https://github.com/choderalab.png","language":"Python","funding_links":[],"categories":["Generative Molecular Design"],"sub_categories":[],"readme":"\u003c!--- [![Travis Build Status](https://travis-ci.org/choderalab/perses.svg?branch=master)](https://travis-ci.org/choderalab/perses/branches) ---\u003e\n[![GH Actions Status](https://github.com/choderalab/perses/workflows/CI/badge.svg)](https://github.com/choderalab/perses/actions?query=branch%3Amaster)\n[![codecov](https://codecov.io/gh/choderalab/perses/branch/main/graph/badge.svg)](https://codecov.io/gh/choderalab/perses/branch/main)\n[![Documentation Status](https://readthedocs.org/projects/perses/badge/?version=latest)](http://perses.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://zenodo.org/badge/27087846.svg)](https://zenodo.org/badge/latestdoi/27087846)\n\n# Perses\n\nExperiments with expanded ensemble simulation to explore chemical and mutational space.\n\n## License\nThis software is licensed under the [MIT license](https://opensource.org/licenses/MIT), a permissive open source license.\n\n## Notice\n\nPlease be aware that this code is made available in the spirit of open science, but is currently pre-alpha--that is,\n**it is not guaranteed to be completely tested or provide the correct results**, and the API can change at any time\nwithout warning. If you do use this code, do so at your own risk. We appreciate your input, including raising issues\nabout potential problems with the code, but may not be able to address your issue until other development activities\nhave concluded.\n\n## Install\n\nSee our installation instructions [here](https://perses.readthedocs.io/en/latest/installation.html).\n\n### Quick Start\n\nIn a fresh conda environment:\n\n```\n$ conda config --add channels conda-forge openeye\n$ conda install perses openeye-toolkits\n```\n\n## Manifest\n\n* `perses/` - Package containing code for performing expanded ensemble simulations\n* `examples/` - Contains examples for various systems and methods of simulation\n* `attic/` - some old code that may be useful as part of the new setup\n* `devtools/` - Continuous integration and packaging utilities\n* `notes/` - LaTeX notes deriving acceptance criteria and stochastic approximation methods\n\n## Contributors\n\nA complete list of contributors can be found at [GitHub Insights](https://github.com/choderalab/perses/graphs/contributors).\n\nMajor contributors include:\n* Julie M. Behr\n* Hannah E. Bruce Macdonald\n* John D. Chodera\n* Patrick B. Grinaway\n* Mike M. Henry\n* Iván J. Pulido\n* Jaime Rodríguez-Guerra\n* Dominic A. Rufa\n* Ivy Zhang\n\n## Cite\nPlease consider citing:\n* **Software**:\n\nRufa, D. A., Zhang, I., Bruce Macdonald, H. E., Grinaway, P. B., Pulido, I., Henry, M. M., Rodríguez-Guerra, J., Wittmann, M., Albanese, S. K., Glass, W. G., Silveira, A., Schaller, D., Naden, L. N., \u0026 Chodera, J. D. (2023). Perses (0.10.3). Zenodo. https://doi.org/10.5281/zenodo.8350218\n\n* **Protein mutations**:\n\nZhang, I., Rufa, D. A., Pulido, I., Henry, M. M., Rosen, L. E., Hauser, K., Singh, S., \u0026 Chodera, J. D. (2023). Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of chemical theory and computation, 19(15), 4863–4882. https://doi.org/10.1021/acs.jctc.3c00333\n\n* **Small molecule transformations**:\n\nRufa, D. A., Bruce Macdonald, H. E., Fass, J., Wieder, M., Grinaway, P. B., Roitberg, A. E., Isayev, O., \u0026 Chodera, J. D. (2020). Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials. In bioRxiv (p. 2020.07.29.227959). https://doi.org/10.1101/2020.07.29.227959\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchoderalab%2Fperses","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchoderalab%2Fperses","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchoderalab%2Fperses/lists"}