SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity

Open source implementation of AlphaFold3

Chai-1, SOTA model for biomolecular structure prediction

Manifold Diffusion Fields

Diffusion on manifolds for image retrieval

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

A curated list of topological deep learning (TDL) resources and links.

[ICLR 2024 Oral] Beyond Weisfeiler-Lehman: A Quantitative Framework for GNN Expressiveness.

Official repository for the Topological Deep Learning Challenge 2024, organized by TAG-DS & PyT-Team and hosted by GRaM Workshop @ ICML 2024.

DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models

This may be the simplest implement of DDPM. You can directly run Main.py to train the UNet on CIFAR-10 dataset and see the amazing process of denoising.

The code for NeurIPS 2023 paper DSR

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper to…

Molecular dynamics simulation plots powered by matplotlib and yaml

Wrapper scripts around MDTraj and VMD for analysing and plotting molecular dynamics simulations.

Google Colab notebooks for running molecular dynamics simulations with GROMACS

Plot the secondary structure of protein residues along a Molecular Dynamics simulation time.

Tools for working with data from molecular dynamics simulations. Trajectory analysis, computational spectroscopy, density plots, distribution functions, atoms/molecules/systems - specializing in aq…

In this repository, we present a simple procedure to perform Free Energy landscape plots, taking results from molecular dynamics simulation.

Two scripts for MD interaction analysis (similar to interaction fraction on desmond).

Repository for Protein-Vec, a protein embedding mixture of experts model

De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds

[TMLR 2023] Training and simulating MD with ML force fields

CLEAN: a contrastive learning model for high-quality functional prediction of proteins

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.