FastMDAnalysis: Software for automated MD trajectory analysis

All-atom generative protein design using SE(3) flow matching

A simple but powerful VSCode extension for visualizing protein structures using the Molstar framework.

Central repository for biomolecular foundation models with shared trainers and pipeline components

Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.

User friendly and accurate binder design pipeline

MMseqs2: ultra fast and sensitive search and clustering suite

Code for running BinderFlow

Benchmark agents on BioML tasks

pip install ipsae

SO3krates and Universal Pairwise Force Field for Molecular Simulation

Rifdock Library for Conformational Search

Plugin for folding sequences directly in PyMOL

Gromacs tutorial PPTs and mdp files, also some plotting scripts

All-Atom Ligand-Conditioned Protein Sequence Design & Sidechain Packing Model

NVIDIA Linux open GPU kernel module source

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

Code for running RFdiffusion

Neural Iterative Selection-Expansion using LASErMPNN and Boltz-1x

Code for designing biased protein states

A computational pipeline for designing protein binders

In silico directed evolution of peptide binders with AlphaFold

Slides + Iframe = sliFrame