quantaosun

Dock-MD-FEP

Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertubation with OpenMM.

Ambertools-OpenMM-MD

Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.

Zinc-Million

Open-Sourced. Millions of small molecules will be downloaded from the ZINC database in 3D SDF file format, with one click, to get ready for a large scale virtual screening for certain protein target.

labodock_binder

Open-sourced, this workflow stands out as one of the premier methods for generating protein-ligand interaction images. With direct accessibility through your browser, it prioritizes enhanced user-friendliness and accessibility.

openmm.py

Open-Sourced: Python script of openmm simulation. For GPU-accelerated molecular dynamics for protein-ligand complex.

gnina

A deep learning framework for molecular docking

labodock

LABODOCK: A Colab-Based Molecular Docking Tools. This fork include modified notebooks that different from its original repo

mordred

a molecular descriptor calculator

pl3_gmx_mmpbsa

Open-Sourced. MMPBSA calculation and binding pocket residue-based energy decomposition after pl3 docking, with gmx_mmpbsa.

webdock

Open-Sourced. Easy docking in your browser without any login requirement. Post processing and interaction diagram included.

ASKCOS_retrosynthesis

Software package for computer aided synthesis planning

chemotion_ELN

Electronic Lab Notebook

covid_classification

(Classification) A very handy neural network model to train a model for covid active small molecule then makes prediction

Dock-MD-BPMD

Open-sourced. A cloud-based workflow to evaluate the confidence of a given docked pose with binding pose metadynamics

pl4

A collection of notebooks for cloud docking, simulation, designing and evaluating new medicinal analogues.

binderhub

Run your code in the cloud, with technology so advanced, it feels like magic!

DoubleG

Open-Sourced. GPU, Gromacs and CharmmGUI three components, makes the Double Gibbs free energy calculation to give one protein-ligand binding free energy.

ExampleNotebooks

Notebooks demonstrating how to do simple tasks related to free energy calculations.

literature_spider

md2googleslides

Generate Google Slides from markdown

mdtraj

An open library for the analysis of molecular dynamics trajectories

Mordred_molecular_descriptors

openvpn

OpenVPN is an open source VPN daemon

overleaf

A web-based collaborative LaTeX editor

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

quantaosun

Reinvent-Linker_PROTAC

SAFEP_tutorial

A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

torchani

Accurate Neural Network Potential on PyTorch

Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program