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esp_dnn

A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces

evis

EViS: an Enhanced Virtual Screening Approach based on Pocket Ligand Similarity

exmol

Explainer for black box models that predict molecule properties

fast

Fusion models for Atomic and molecular STructures (FAST)

fegrow

An Open-Source Molecular Builder and Free Energy Preparation Workflow

fesetup

A tool for setting up free energy simulations.

freenrgworkflows

Software for automated processing of alchemical free energy calculations

g_mmpbsa

MM-PBSA method for GROMACS. For full description, please visit homepage:

gentrl

Generative Tensorial Reinforcement Learning (GENTRL) model

geodiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

global-chem

A Chemical Knowledge Graph of What is Common in the World.

gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

gmxtool

tools for GROMACS

gnina

A deep learning framework for molecular docking

graphbp

Official implementation of "Generating 3D Molecules for Target Protein Binding"

gromacs_ff

Trusted force field files for gromacs

gromacs_py

Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a pdb file, create the simulation system (box, add water and ions) and run minimisation, equilibration and production run.

hotspots

A knowledge-based method for determining small molecule binding "hotspots".

ili

Web-based software for visualization of molecular maps in 2D and 3D

interactiongraphnet

InteractionGraphNet: a Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein-Ligand Interaction Prediction and Large-scale Structure-based Virtual Screening

intro_dgm

An Introduction to Deep Generative Modeling: Examples

ipymol

Control PyMOL sessions via IPython

jupyter_dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

kinfraglib

Kinase-focused fragment library

kinodata

Collection of scripts / notebooks to reliably select datasets

kissim

Subpocket-based fingerprint for kinase pocket comparison

lib-invent-dataset

ligan

Deep generative models of 3D grids for structure-based drug discovery

making-it-rain

Cloud-based molecular simulations for everyone

md-scripts

A collections of scripts for working molecular dynamics simulations