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This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) ca…
Advanced Python Mastery (course by @dabeaz)
Auto3D generates low-energy conformers from SMILES/SDF
Resources, Code, and Other things I use to teach Cheminformatics.
Advanced toolkit for binding free energy calculations
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
AutoDock for GPUs and other accelerators
Practical Cheminformatics Tutorials
Simulation-Enabled Estimation of Kinetic Rates - Version 2
Unified biological sequence manipulation in Python
Set up relative free energy calculations using a common scaffold
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
Python package designed for general financial and security returns analysis.
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
A curated list of awesome ARKit projects and resources. Feel free to contribute!
RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on…
Dockerizing Django with Postgres, Gunicorn, and Nginx
3D molecular structure generation for MD simulation
Synthesis of molecules from fragments into larger molecules using graph-based representations and techniques.
A script to run structural alerts using the RDKit and ChEMBL
The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.