Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3

A trainable PyTorch reproduction of AlphaFold 3.

Proteina is a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture.

Foldseek enables fast and sensitive comparisons of large structure sets.

A standardized protein design benchmark for motif-scaffolding problems

A package to create, visualize, and analysis PDB-derived pseudo-ensembles.

Sidechain conditioning and modeling for full-atom protein sequence design

Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

Distribution package for BaNDyT: Bayesian Network Analysis of Dynamic Trajectories

Diffusion-based all-atom protein generative model.

A generative model for programmable protein design

Protein Ligand INteraction Dataset and Evaluation Resource

Comprehensive benchmarking of protein-ligand structure prediction methods (ICML 2024 AI4Science)

Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes

Parse and tag unstructured academic citations.

An open library for the analysis of molecular dynamics trajectories

This is a package for doing history-augmented MSM (haMSM) analysis on weighted ensemble trajectories.

A general framework for inference-time scaling and steering of diffusion models with arbitrary rewards.

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

User friendly and accurate binder design pipeline

NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.

Code for TFG: Unified Training-Free Guidance for Diffusion Models

Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction (CASP16)

Menubar Tool to set Charge Limits and Prolong Battery Lifespan

A benchmark for 3D biomolecular structure prediction models

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation