Tools for co-folding protein-ligand complexes
NeuralPLexer
Date: 12-Feb-24
Paper: State-specific proteinâligand complex structure prediction with a multiscale deep generative model
Task: protein-small mol
DOI: https://doi.org/10.1038/s42256-024-00792-z
Code: https://github.com/zrqiao/NeuralPLexer
RosettaFold-AA
Date: 7-Mar-24
Paper: Generalized biomolecular modeling and design with RoseTTAFold All-Atom
Task: all atoms
DOI: https://doi.org/10.1126/science.adl2528
Code: https://github.com/baker-laboratory/RoseTTAFold-All-Atom
AlphaFold3
Date: 8-May-24
Paper: Accurate structure prediction of biomolecular interactions with AlphaFold 3
Task: all atoms
DOI: https://doi.org/10.1038/s41586-024-07487-w
Code: https://github.com/google-deepmind/alphafold3
Umol
Date: 28-May-24
Paper: Structure prediction of protein-ligand complexes from sequence information with Umol
Task: protein-small mol
DOI: https://doi.org/10.1038/s41467-024-48837-6
Code: https://github.com/patrickbryant1/Umol
HelixFold3
Date: 30-Aug-24
Paper: Technical Report of HelixFold3 for Biomolecular Structure Prediction
Task: all atoms
DOI: https://doi.org/10.48550/arXiv.2408.16975
Code: https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3
Chai
Date: 15-Oct-24
Paper: Chai-1: Decoding the molecular interactions of life
Task: all atoms
DOI: https://doi.org/10.1101/2024.10.10.615955Â
Code: https://github.com/chaidiscovery/chai-lab/
Boltz-1
Date: 27-Dec-24
Paper: Boltz-1: Democratizing Biomolecular Interaction Modeling
Task: all atoms
DOI: https://doi.org/10.1101/2024.11.19.624167
Code: https://github.com/jwohlwend/boltz
Protenix
Date: 11-Jan-25
Paper: Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction
Task: all atoms
DOI: https://doi.org/10.1101/2025.01.08.631967Â
Code: https://github.com/bytedance/Protenix
Boltz-2
Date: 18-Jun-25
Paper: Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction
Task: all atoms
DOI: https://doi.org/10.1101/2025.06.14.659707
Code: https://github.com/jwohlwend/boltz