agoliaei

hremd-idp

implicit_solvent

Using OpenMM to test how well AMBER + implicit solvent can re-rank docked poses

westpa2_tutorials

Advanced tutorials for WESTPA 2.0

AlGDock

Molecular docking with Alchemical Interaction Grids

seekr2

Simulation-Enabled Estimation of Kinetic Rates - Version 2

ABFE_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.

pysb-units

PySB add-on providing utilities to add units to models and perform dimensional analysis.

pytorch-original-transformer

My implementation of the original transformer model (Vaswani et al.). I've additionally included the playground.py file for visualizing otherwise seemingly hard concepts. Currently included IWSLT pretrained models.

forcebalance

Systematic force field optimization.

LLMs-from-scratch

Implementing a ChatGPT-like LLM in PyTorch from scratch, step by step

bgmol

Molecular mechanics systems and simulation data

bgflow

Boltzmann Generators and Normalizing Flows in PyTorch

improved-t5

Experiments for efforts to train a new and improved t5

simple-simulate-complex

Simple protein-ligand complex simulation with OpenMM

jaxton

100 exercises to learn JAX

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 AMBER and OpenMM simulation packages.

sire

Sire Molecular Simulations Framework

practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

dockECR

dockECR: open consensus docking and ranking protocol for virtual screening of small molecules

deepmd-kit

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

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

torchmd-cg

Example to fit parameters and run CG simulations using TorchMD and Schnet

RITA

RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Marks Lab at Harvard.

PGP

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

TDC

Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science

AutoDock-GPU

AutoDock for GPUs and other accelerators

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.

making-it-rain

Cloud-based molecular simulations for everyone

Making-it-rain

Cloud-based molecular simulations for everyone