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100-days-of-ml-code

100 Days of ML Coding

2022-10-10-ucsd

R, Unix Shell, & Git Workshop

30-days-of-python

30 days of Python programming challenge is a step-by-step guide to learn the Python programming language in 30 days. This challenge may take more than100 days, follow your own pace.

awesome-python-chemistry

A curated list of Python packages related to chemistry

cellpack

chimerax_moleculardynamicviewer

A simple multiframe PDB viewer for ChimeraX

covid

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

delta-ood-jupyterlab

esm

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

folding_tools

A collection of *fold* tools

foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

gamd-openmm

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/

gamd-openmm-examples

learn-python

📚 Playground and cheatsheet for learning Python. Collection of Python scripts that are split by topics and contain code examples with explanations.

loos

LOOS: a lightweight object-oriented structure analysis library

making-it-rain

Cloud-based molecular simulations for everyone

manifoldem_python

ManifoldEM Python suite

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

mdfret

R package for analysis of MD files in relation to FRET values.

meeko

Interfacing RDKit and AutoDock

molecularnodes

Addon and nodes for working with structural biology and molecular data in Blender.

msm_we

History-augmented Markov analysis of weighted ensemble trajectories.

napari

napari: a fast, interactive, multi-dimensional image viewer for python

notebook

Jupyter Interactive Notebook

papers_for_protein_design_using_dl

List of papers about Proteins Design using Deep Learning

practical-python

Practical Python Programming (course by @dabeaz)

project-based-learning

Curated list of project-based tutorials

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA

pyreweighting