AnthonyBogetti
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ProDy Public
Forked from prody/ProDyA Python Package for Protein Dynamics Analysis
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SimpleSimulationTools Public
A collection of codes for running enhanced sampling simulations. No installation needed. Interoperable with any dynamics package. Simple code that is readable and free.
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meld-ae Public
MELD-AE (Anthony's Edition): A minimal MELD package that uses Amber's REMD code.
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meld Public
Forked from maccallumlab/meldModeling with limited data
Python Other UpdatedFeb 3, 2025 -
meld_tutorials Public
This repo is a collection of minimal MELD tutorials for new and advanced users. I have implicit/explicit versions and also show how to run conventional MD, T-REMD and T,H-REMD all using MELD.
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MABL Public
A framework for minimal adaptive binless methods for weighted ensemble simualtions.
3 UpdatedDec 6, 2024 -
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prody-feedstock Public
Forked from conda-forge/prody-feedstockA conda-smithy repository for prody.
BSD 3-Clause "New" or "Revised" License UpdatedNov 5, 2024 -
westpa Public
Forked from westpa/westpaWESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
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westpa-workshop2024-tutorials Public
Forked from jeremyleung521/westpa-workshop2024-tutorialsWESTPA Workshop 2024 Tutorial Files
Jupyter Notebook UpdatedJun 17, 2024 -
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user_submitted_scripts Public
Forked from westpa/user_submitted_scriptsExample scripts for WESTPA submitted by users
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LPATH Public
Forked from jeremyleung521/LPATHA user-friendly, Python tool for clustering pathways from molecular dynamics simulations
Python MIT License UpdatedAug 17, 2023 -
westpa_tutorials Public
Forked from westpa/westpa_tutorialsTutorials and additional documentation for the WESTPA suite
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pathway_class_finder Public
Workflow for using pattern matching to identify distinct pathway classes from WE simulations
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data_coding_exercise Public
A repository containing my scripts and outputs for the data coding exercise.
Python UpdatedOct 28, 2022 -
westpa_resamplers Public
A collection of resamplers for the weighted ensemble software package WESTPA
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mdlearn Public
Forked from ramanathanlab/mdlearnMachine learning for molecular dynamics
Python MIT License UpdatedAug 2, 2022 -
westpa2_tutorials Public
Forked from westpa/westpa2_tutorialsTutorials and additional documentation for the WESTPA 2.0. (For future LiveCoMS Tutorial Paper)
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machine-learning Public
Machine learning for hybrid QM/MM simulations run with the weighted ensemble strategy
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wepy Public
Forked from ADicksonLab/wepyWeighted Ensemble simulation framework in Python
Python MIT License UpdatedSep 28, 2021 -
westpa_post_sim_recycling Public
A script that can recycle post-WE simulation.
Python UpdatedAug 13, 2021 -
rhapsody Public
Forked from prody/rhapsodyPython program, based on Prody, for pathogenicity prediction of human missense variants
Python GNU General Public License v3.0 UpdatedJun 29, 2021 -
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WestpaTools Public
A python-based suite of analysis and visualization for WESTPA.
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WESTPASetupWizard Public
Forked from 21clshao96/WESTPASetupWizardA Jupyter Notebook script dedicated to helping users more easily setup a WESTPA simulation.