{"payload":{"pageCount":5,"repositories":[{"type":"Public","name":"pymbar","owner":"choderalab","isFork":false,"description":"Python implementation of the multistate Bennett acceptance ratio (MBAR)","allTopics":["research","pymbar","equilibrium","molecular-dynamics-simulations","single-molecule-pulling","multistate-bennett-acceptance-ratio","bennett-acceptance-ratio","extended-bridge-sampling","python","free-energies","thermodynamic-states","mbar"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":10,"issueCount":111,"starsCount":234,"forksCount":90,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-28T14:28:31.015Z"}},{"type":"Public","name":"modelforge","owner":"choderalab","isFork":false,"description":"Infrastructure to implement and train NNPs","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":10,"issueCount":12,"starsCount":11,"forksCount":4,"license":"MIT License","participation":[5,10,19,6,8,5,21,6,4,14,0,0,0,1,0,0,0,0,0,0,0,1,1,1,0,1,4,10,7,10,13,20,3,10,18,9,5,12,18,9,7,6,9,12,30,6,34,23,40,47,22,3],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-29T14:39:28.243Z"}},{"type":"Public","name":"missense-kinase-toolkit","owner":"choderalab","isFork":false,"description":"An ETL pipeline package to facilitate structure-based ML for missense human kinase property prediction","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,15,2,0,0,0,0,3,2,0,0,7,10,0,2,0,6,0,2,0,1,0,0,0,0,1,0,0,8],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-27T22:02:48.400Z"}},{"type":"Public","name":"openmmtools","owner":"choderalab","isFork":false,"description":"A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.","allTopics":["molecular-dynamics","mcmc","markov-chain-monte-carlo","alchemical-free-energy-calculations","replica-exchange","integrators","python","openmm","molecular-simulations","free-energy-calculations"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":29,"issueCount":210,"starsCount":243,"forksCount":76,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-27T14:44:23.880Z"}},{"type":"Public","name":"feflow","owner":"choderalab","isFork":false,"description":"Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":5,"issueCount":22,"starsCount":13,"forksCount":1,"license":"MIT License","participation":[0,0,0,5,12,9,9,0,0,2,0,0,5,9,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,5,2,0,2,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-29T22:44:30.530Z"}},{"type":"Public","name":"machine_learned_potential_experiments","owner":"choderalab","isFork":false,"description":"Perform experiments with modelforge","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-19T18:09:32.380Z"}},{"type":"Public","name":"mtenn","owner":"choderalab","isFork":false,"description":"Modular Training and Evaluation of Neural Networks","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":4,"starsCount":5,"forksCount":1,"license":"MIT License","participation":[2,0,0,1,7,0,25,1,5,1,3,0,3,2,1,0,0,1,5,4,9,39,6,34,10,0,2,0,28,5,1,8,31,9,9,3,0,0,0,0,0,0,0,0,7,4,10,1,5,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-23T09:19:47.993Z"}},{"type":"Public","name":"espaloma_charge","owner":"choderalab","isFork":false,"description":"Standalone charge assignment from Espaloma framework.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":14,"starsCount":37,"forksCount":5,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-12T22:25:10.536Z"}},{"type":"Public","name":"refit-espaloma","owner":"choderalab","isFork":false,"description":"Refit espaloma with energies and forces","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":8,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-16T03:34:25.160Z"}},{"type":"Public","name":"espaloma","owner":"choderalab","isFork":false,"description":"Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹<a href=\"https://arxiv.org/abs/2010.01196\" rel=\"nofollow\">https://arxiv.org/abs/2010.01196</a>","allTopics":["graph-learning","forcefield-parameterization"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":14,"issueCount":51,"starsCount":208,"forksCount":23,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-19T18:58:35.400Z"}},{"type":"Public","name":"espfit-experiment","owner":"choderalab","isFork":false,"description":"Workspace for espfit","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-16T13:29:36.543Z"}},{"type":"Public","name":"harbor","owner":"choderalab","isFork":false,"description":"A home for docking evaluation and assessment","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":1,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T18:40:16.903Z"}},{"type":"Public","name":"asapdiscovery-ml-eval","owner":"choderalab","isFork":false,"description":"Tools for retrospective and propsective evaluation of ASAP ML models","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-12T19:35:04.443Z"}},{"type":"Public","name":"espfit","owner":"choderalab","isFork":false,"description":"Refit espaloma with quantum chemical data and condensed phase properties of RNA systems","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":6,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-07T20:20:58.153Z"}},{"type":"Public","name":"chiron","owner":"choderalab","isFork":false,"description":"Differentiable Markov Chain Monte Carlo","allTopics":["molecular-dynamics"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":16,"starsCount":14,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-23T06:19:12.428Z"}},{"type":"Public","name":"rbd-ace2-xbb15-simulations","owner":"choderalab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Creative Commons Zero v1.0 Universal","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-14T20:33:23.650Z"}},{"type":"Public","name":"perses","owner":"choderalab","isFork":false,"description":"Experiments with expanded ensembles to explore chemical space","allTopics":["molecular-dynamics","openmm","molecular-design","free-energy-perturbation","relative-free-energy","python","simulation","expanded-ensembles"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":6,"issueCount":221,"starsCount":179,"forksCount":50,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-19T21:52:24.938Z"}},{"type":"Public","name":"vanilla-espaloma-experiment","owner":"choderalab","isFork":false,"description":"Vanilla MD simulation of protein-ligand complex using espaloma-0.3","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-12T15:26:39.414Z"}},{"type":"Public","name":"pl-benchmark-espaloma-experiment","owner":"choderalab","isFork":false,"description":"Alchemical protein-ligand benchmark experiment using Perses and espaloma force field","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-12T15:25:49.425Z"}},{"type":"Public","name":"papers-and-grants","owner":"choderalab","isFork":false,"description":"YAML database of papers and grants from the Chodera lab","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Creative Commons Zero v1.0 Universal","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-06T22:37:19.471Z"}},{"type":"Public","name":"auditorium","owner":"choderalab","isFork":false,"description":"Perform benchmark and stability tests foe a set of NNPs","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-08T15:38:30.501Z"}},{"type":"Public","name":"ffsettings","owner":"choderalab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-01T17:16:46.240Z"}},{"type":"Public","name":"yank","owner":"choderalab","isFork":false,"description":"An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.","allTopics":["molecular-dynamics","openmm","molecular-dynamics-simulation","drug-discovery","free-energy","free-energy-perturbation","alchemical-free-energy-calculations","alchemical","python","mskcc"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":8,"issueCount":235,"starsCount":177,"forksCount":70,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-06T21:24:34.010Z"}},{"type":"Public","name":"asapdiscovery-mers-docking","owner":"choderalab","isFork":false,"description":"Repo for the code used in a paper for docking predictions to MERS Mpro","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Creative Commons Zero v1.0 Universal","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-05T17:53:04.203Z"}},{"type":"Public","name":"mpiplus","owner":"choderalab","isFork":false,"description":" Utilities to run on MPI.","allTopics":["python","mpi","openmm","yank","openmmtools"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":3,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-27T17:30:16.538Z"}},{"type":"Public","name":"pdbbind_ml","owner":"choderalab","isFork":false,"description":"Scripts to train and evaluate ML models on the PDBBind dataset.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-31T20:49:33.976Z"}},{"type":"Public","name":"gimlet","owner":"choderalab","isFork":false,"description":"Graph Inference on MoLEcular Topology","allTopics":["graph-theory","tensorflow-gpu","molecular-modeling"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":26,"forksCount":9,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-25T00:21:46.498Z"}},{"type":"Public","name":"sake","owner":"choderalab","isFork":true,"description":"Spatial Attention Kinetic Networks with E(n)-Equivariance","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":4,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-01T15:25:31.996Z"}},{"type":"Public","name":"malt","owner":"choderalab","isFork":true,"description":"Molecular Active Learning Testbed","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-10T21:45:38.743Z"}},{"type":"Public","name":"espalomax","owner":"choderalab","isFork":false,"description":"Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹<a href=\"https://arxiv.org/abs/2010.01196\" rel=\"nofollow\">https://arxiv.org/abs/2010.01196</a>","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-21T04:51:53.230Z"}}],"repositoryCount":139,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"choderalab repositories"}