ytworks

pytorch_forward_forward

Implementation of Hinton's forward-forward (FF) algorithm - an alternative to back-propagation

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

ColabDesign

Making Protein Design accessible to all via Google Colab!

REINVENT4

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

ASE_ANI

ANI-1 neural net potential with python interface (ASE)

posebusters

Plausibility checks for generated molecule poses.

espsim

Scoring of shape and ESP similarity with RDKit

openfe

The Open Free Energy toolkit

FEgrow

An Open-Source Molecular Builder and Free Energy Preparation Workflow

fep-benchmark

Benchmark set for relative free energy calculations.

jazzy

Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules.

qligfep

TS

Thompson Sampling

af2bind

DeepICL

Official Github for "3D Molecular Generative Framework for Interaction-guided Drug Design" (Nature Communications)

piston

Evaluating Protein Binding Interfaces with Transformer Networks

GIGN

alphafold-multistate

public_binding_free_energy_benchmark

The public versio

genesis

Source, test set, and document for Molecular Dynamics software, GENESIS.

BioSimSpaceTutorials

Uni-pKa

The official repository of Uni-pKa

WSME-L_model

antibody-mutations

Assessing the impact of mutations on antibody-antigen binding affinity

perses_protein_mutations

testing and benchmarking perses protein mutations

ion_solvation_openmm

Ion solvation free energy with spherical boundary conditions

chem

TIES

Topology Superimposition based on joint graph traversal

TIES_analysis

Python package to perform analysis on output energies from TIES programs.

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling