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3d-generative-sbdd

💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)

alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

autofinger

This script automatically takes the csv file from schrodinger-maestro and converts it into a table for data analysis and publication

bar-fep

BAR and FEP method for free energy calculation

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER20 and OpenMM 7 simulation packages.

benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

bio_embeddings

Get protein embeddings from protein sequences

biogpt

dash_web

deepbind

Machine learning model for predicting the effection of point mutation to protein-protein binding free energy

deepfe-ppi

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

deepprotacs

delinker

dftbplus

DFTB+ general package for performing fast atomistic simulations

dpdispatcher

generate HPC scheduler systems jobs input scripts and submit these scripts to HPC systems and poke until they finish

drug-molecule-properties

Project to predict drug molecules properties with Deep Learning

drug_design_models

This project is a reimplementation of the models introduced in the following papers: "Multiobjective de novo drug design with recurrent neural networks and nondominated sorting", "REINVENT 2.0: An AI Tool for De Novo Drug Design", "Hierarchical generation of molecular graphs using structural motifs", "Mol-CycleGAN: a generative model for molecular optimization", "Multi-objective de novo drug design with conditional graph generative model" and "Graph convolutional policy network for goal-directed molecular graph generation".

drugood

OOD Dataset Curator and Benchmark for AI-aided Drug Discovery

esm

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

excape

Code for DNNs in the ExCAPE-Project

fastmbar

A fast solver for large scale MBAR/UWHAM equations

fep-benchmark

Benchmark set for relative free energy calculations.

flask-dash

A template repo to rapidly build and deploy web apps for data science projects. Built with Flask and Dash on a PostgreSQL database, complete with a user login.

fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in

freesolv

Experimental and calculated small molecule hydration free energies

fxmolviewer

JavaFX based viewer and editor for molecules and proteins with surfaces

geodiff

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

geom-cvae

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science