PeterBernoulli

plinder

Protein Ligand INteraction Dataset and Evaluation Resource

alphafold3-pytorch

Implementation of Alphafold 3 in Pytorch

kornia

Geometric Computer Vision Library for Spatial AI

ThinkMatch

A research protocol for deep graph matching.

active_sciencing

active learning + reusable workflows + likelihood free inference

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

gvp-pytorch

Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

geometric-gnn-dojo

Geometric GNN Dojo provides unified implementations and experiments to explore the design space of Geometric Graph Neural Networks.

ConPLex

Adapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.

two-for-one-diffusion

This Denoising Force Field (DFF) codebase provides a Pytorch framework for the method presented in Two for one: Diffusion models and force fields for coarse-grained molecular dynamics.

awesome-equivariant-network

Paper list for equivariant neural network

nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

se3_diffusion

Implementation for SE(3) diffusion model with application to protein backbone generation

pytorch-CycleGAN-and-pix2pix

Image-to-Image Translation in PyTorch

NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

generative-models

Generative Models by Stability AI

onnxruntime

ONNX Runtime: cross-platform, high performance ML inferencing and training accelerator

the-art-of-command-line

Master the command line, in one page

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

LP-PDBBind

Graph-Matching-Networks

PyTorch implementation of Graph Matching Networks, e.g., Graph Matching with Bi-level Noisy Correspondence (COMMON, ICCV 2023), Graph Matching Networks for Learning the Similarity of Graph Structured Objects (GMN, ICML 2019).

GMN

[ICLR 2022] The implementation for the paper "Equivariant Graph Mechanics Networks with Constraints".

DynamicBind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

LLMRec

[WSDM'2024 Oral] "LLMRec: Large Language Models with Graph Augmentation for Recommendation"

FlexPose

FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.

chroma

A generative model for programmable protein design

awesome-docking

An awesome & curated list of docking papers

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data