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Python 6 1 Updated Dec 7, 2024

A curated list of awesome computational cryo-EM methods.

Jupyter Notebook 105 12 Updated Oct 23, 2024

The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

Jupyter Notebook 6 Updated Dec 30, 2024
C++ 33 27 Updated Dec 16, 2024
Python 3 1 Updated May 23, 2023

Cryo electron microscopy image simulation and analysis built on JAX.

Python 31 13 Updated Dec 19, 2024

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)

Python 31 9 Updated Jul 17, 2024

Neural networks for cryo-EM reconstruction

Python 328 78 Updated Dec 30, 2024

STAR file I/O in Python

Python 48 19 Updated Nov 18, 2024
Python 3 Updated May 23, 2023

GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the characterization of structural models with respect to indivi…

C++ 11 3 Updated Apr 7, 2023

Force fields in various formats

Python 26 23 Updated May 2, 2024

Python package for determination of conformational continua of macromolecules from single-particle cryo-EM data

Python 7 1 Updated Dec 5, 2024

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Python 3,352 659 Updated Feb 7, 2024

A unified framework for machine learning collective variables for enhanced sampling simulations

Python 95 27 Updated Dec 23, 2024

Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"

Roff 19 10 Updated Jun 6, 2024

🧬 gget enables efficient querying of genomic reference databases

Python 960 75 Updated Dec 30, 2024

Spectral Gap Optimization of Parameters

Jupyter Notebook 17 7 Updated Mar 28, 2020

A zotero plugin to automatically merge duplicate items

JavaScript 346 11 Updated Aug 13, 2024

Improved vim spelling plugin (with camel case support)!

Vim Script 363 21 Updated Jul 19, 2024

Python implementation of the umbrella integration method for potential of mean force (PMF) calculations

Python 15 7 Updated Feb 4, 2019

A python implementation of the string method with swarms of trajectories using GROMACS

Python 18 5 Updated Oct 19, 2022
Python 1 Updated Feb 18, 2022

A python toolkit for analysing membrane protein-lipid interactions.

Python 63 29 Updated Apr 17, 2023

Python implementation of Dynamical Network Analysis

Python 13 1 Updated Aug 23, 2023
Jupyter Notebook 1 Updated Dec 8, 2021

LOOS: a lightweight object-oriented structure analysis library

C++ 122 25 Updated Nov 7, 2024

Python code for generating Boresch restraints from MD simulations

Python 18 6 Updated Aug 9, 2022
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