Papers and Resources

De-Novo Structure and Binder Design/Diffusion

RFDiffusion Paper

RFDiffusion2

DDPMs paper

BindCraft

Structure Prediction 

AlphaFold2/AlphaFold3

RosettaFold

Boltz

Chai

OpenFold2/OpenFold3

SeedFold

Structure-Based Sequence Design

ProteinMPNN

LigandMPNN

ESM-IF1

EvoPro

AntiFold

Protein Language Model Related

ESM2 and ESMFold

ESMC and ESMFold2

ProGen2

IgLM

Rosetta-Related

Top7

Rosetta3

Ref2015

Rosie Web Server/Protocol (example docking protocol)