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automatic drug design

args

A simple header-only C++ argument parser library. Supposed to be flexible and powerful, and attempts to be compatible with the functionality of the Python standard argparse library (though not necessarily the API).

asyncio-example

Artifacts made during asyncio workshops at PyConPL 2016

awesome-cheatsheets

📚 Awesome cheatsheets for popular programming languages, frameworks and development tools. They include everything you should know in one single file.

awesome-molecular-dynamics

:sunglasses: A curated list of awesome Molecular Dynamics libraries, tools and software.

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

brutereg

core-av3

deep-reinforcement-learning

Repo for the Deep Reinforcement Learning Nanodegree program

densepcr

Repository for 'Dense 3D Point Cloud Reconstruction Using a Deep Pyramid Network' [WACV 2019]

desmond-gist

Implementation of grid inhomogeneous solvation theory in python

desmond-hsa

Hydration site analysis scripts for Desmond trajectories

docker-clean_up

docker-opengl

A docker image that supports rendering graphical applications.

e3fp

3D molecular fingerprints

easypymol

Script to facilitate the making of horizontal scripts

examples

example_files

fastoverlap

Algorithms for fast alignment of structures in finite and periodic systems.

foldingdiff

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

fragfeature

freesolv

See http://www.escholarship.org/uc/item/6sd403pz

gcmc-lennardjones

Grand Canonical Monte Carlo Simulation of supercritical Lennard-Jones fluid

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

gibs

GIBS: Grand Canonical Monte Carlo (GCMC) simulation program for simulating ion-biomolecule interactions with molecular solvent models

gnina

gnina is not smina/vina

gpu-passthrough-tutorial

gpu-tests

Some GPU tests on textures

hipart

HiPart is a program to analyze the electronic structure of molecules with fuzzy-atom partitioning methods.

hop

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

jobengine

Manage MD simulations across multiple computing clusters