atbogetti
Postdoctoral researcher working jointly in the Dill and Bahar labs at the Laufer Center at Stony Brook University. Working on MD methods and enhanced sampling.
Laufer Center for Physical and Quantitative BiologyStony Brook, NY
Pinned Repositories
dotfiles
Configuration files for my linux desktops
ltchong.github.io
machine-learning
Machine learning for hybrid QM/MM simulations run with the weighted ensemble strategy
odld
A simple tests system for WESTPA testing and debugging
pathway_class_finder
Workflow for using pattern matching to identify distinct pathway classes from WE simulations
ProDy
A Python Package for Protein Dynamics Analysis
westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
westpa2_tutorials
Tutorials and additional documentation for the WESTPA 2.0. (For future LiveCoMS Tutorial Paper)
westpa_resamplers
A collection of resamplers for the weighted ensemble software package WESTPA
westpa_tutorials
Tutorials and additional documentation for the WESTPA suite
atbogetti's Repositories
atbogetti/pathway_class_finder
Workflow for using pattern matching to identify distinct pathway classes from WE simulations
atbogetti/odld
A simple tests system for WESTPA testing and debugging
atbogetti/westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
atbogetti/westpa_resamplers
A collection of resamplers for the weighted ensemble software package WESTPA
atbogetti/dotfiles
Configuration files for my linux desktops
atbogetti/ltchong.github.io
atbogetti/machine-learning
Machine learning for hybrid QM/MM simulations run with the weighted ensemble strategy
atbogetti/ProDy
A Python Package for Protein Dynamics Analysis
atbogetti/user_submitted_scripts
Example scripts for WESTPA submitted by users
atbogetti/westpa2_tutorials
Tutorials and additional documentation for the WESTPA 2.0. (For future LiveCoMS Tutorial Paper)
atbogetti/westpa_tutorials
Tutorials and additional documentation for the WESTPA suite
atbogetti/WESTPASetupWizard
A Jupyter Notebook script dedicated to helping users more easily setup a WESTPA simulation.
atbogetti/WestpaTools
A python-based suite of analysis and visualization for WESTPA.
atbogetti/LPATH
A user-friendly, Python tool for clustering pathways from molecular dynamics simulations
atbogetti/atbogetti.github.io
atbogetti/data_coding_exercise
A repository containing my scripts and outputs for the data coding exercise.
atbogetti/DruGUI
Druggability Suite
atbogetti/mdlearn
Machine learning for molecular dynamics
atbogetti/meld
Modeling with limited data
atbogetti/my-program
atbogetti/rhapsody
Python program, based on Prody, for pathogenicity prediction of human missense variants
atbogetti/wepy
Weighted Ensemble simulation framework in Python
atbogetti/westpa-workshop2024-tutorials
WESTPA Workshop 2024 Tutorial Files
atbogetti/westpa_post_sim_recycling
A script that can recycle post-WE simulation.