BoltzGen: Toward Universal Binder Design

Codes for our paper "Full-Atom Peptide Design with Geometric Latent Diffusion" (NeurIPS 2024)

Codes for our paper "UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design" (ICML 2025)

Codes for our paper "Programming Biomolecular Interactions with All-Atom Generative Model"

Automated generation of immunogenic peptides from protein structures and molecular docking analysis using AlphaFold2 and AutodockVina.

A modular, extensible peptide design pipeline with target preparation, backbone generation, sequence design, scoring, and ranking. Full local CPU pipeline, and backend hooks for RFpeptides, ProteinMPNN/LigandMPNN, and ColabFold.

GFlowNet-based therapeutic peptide design. Generates diverse, high-quality candidates (5.4x better diversity vs PPO/GRPO) to reduce correlated wet-lab failures. Published method with pre-trained models. Validated on FLIP & Propedia benchmarks.

Source code for Targeting SARS-CoV-2 Receptor Binding Domain and Main Protease with D-peptides

Rosetta MCP for cyclic peptide design with kic

RFpeptides MCP server for peptide design

Evaluation other methods for macrocyclic design

CyclicCHAMP MCP server for cyclic peptide modeling

HighFold3 MCP server for peptide structure prediction

PharmPApp MCP server for pharmaceutical peptide property prediction

MultiCycPermea MCP server for cyclic peptide permeability prediction

MultiCycGT MCP server for multi-cyclic peptide generation

PepFlowww MCP server for peptide flow-based design

Cyclic peptide MCP server for cyclic peptide design and analysis

CPMP MCP server for cyclic peptide membrane permeability prediction

AMP Forge is an antimicrobial peptide generation project based on PLM embeddings, VAE, and latent diffusion.