A standardized protein design benchmark for motif-scaffolding problems

Sidechain conditioning and modeling for full-atom protein sequence design

Uniform Manifold Approximation and Projection

Official implementation of SketchMol.

Molecular dynamics simulations with an LLM agent

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

Comprehensive ensembling of protein-ligand structure and affinity prediction methods (CASP16)

Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!

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

A pipeline that used ML model based on Rosetta descriptors to predict the binding affinity of protein-protein complexes

Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2

protein structure generation with sparse all-atom denoising models

Making Protein Design accessible to all via Google Colab!

Parameter/topology editor and molecular simulator

A tool for protein and protein complex structure prediction.

A framework for text-guided protein design

A collection of tutorials for the python implementation of Bayesian Network analysis of Dynamic Trajectories

Distribution package for BaNDyT: Bayesian Network Analysis of Dynamic Trajectories

A comprehensive library for computational molecular biology

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Repo containing demo to recreate Ion Sampling and designs discussed in 2023 Rosetta SPaDES submission