Miro-Astore

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Miro Astore's starred repositories

esm

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

Language:PythonMIT3177 64 320

gget

🧬 gget enables efficient querying of genomic reference databases

Language:PythonBSD-2-Clause933 11 68

spelunker.vim

Improved vim spelling plugin (with camel case support)!

Language:Vim scriptMIT358 4 48

ZoteroDuplicatesMerger

A zotero plugin to automatically merge duplicate items

Language:JavaScriptMPL-2.0331 7 15

cryodrgn

Neural networks for cryo-EM reconstruction

Language:PythonGPL-3.0312 13 275

loos

LOOS: a lightweight object-oriented structure analysis library

Language:C++GPL-3.0122 16 49

mlcolvar

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

Language:PythonMIT91 7 73

PyLipID

A python toolkit for analysing membrane protein-lipid interactions.

Language:PythonMIT59 3 26

starfile

STAR file I/O in Python

Language:PythonBSD-3-Clause44 3 25

cisTEM

Language:C++NOASSERTION32 7 327

cryojax

Cryo electron microscopy image simulation and analysis built on JAX.

Language:PythonLGPL-2.129 6 102

cg2at

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

Language:PythonGPL-3.029 4 14

force_fields

Force fields in various formats

Language:Python25 11 2

deep-learning-slow-modes

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

Language:Roff19 2 3

string-method-swarms-trajectories

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

Language:PythonMIT17 6 16

MDRestraintsGenerator

Python code for generating Boresch restraints from MD simulations

Language:PythonLGPL-3.017 4 24

SGOOP

Spectral Gap Optimization of Parameters

Language:Jupyter NotebookMIT17 5 2

umbrella_integration

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

Language:PythonGPL-3.015 20

dynetan

Python implementation of Dynamical Network Analysis

Language:PythonGPL-3.013 3 12

BioEM

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 individual electron microscopy images.

Language:C++NOASSERTION11 2 2

Ensemble-reweighting-using-Cryo-EM-particles

Language:Jupyter NotebookMIT10 8 3

Hbond-analysis

Jupyter notebook for Hbond analysis and tcl script to display Hbond stability in VMD

Language:Jupyter Notebook7 10

POLARIS

Path of least action analysis on energy landscapes

Language:PythonGPL-3.06 2 11

Cryo-EM-Heterogeneity-Challenge-1

The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

Language:Jupyter NotebookMIT5 7 45

bioem_toolkit

Language:Python3 10

BOTalign

Language:Python300

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

Language:PythonNOASSERTION2 10

plumed-patch-grest-stringmethod

Language:C++1 2 1

atb_api

Language:PythonMIT1 20

dynamic_network_analysis_scripts

Language:Jupyter NotebookMIT1 20