Structure Prediction Tools
trRosetta
Date: 2-Jan-20
Target: Proteins
Paper: Improved protein structure prediction using predicted interresidue orientations
DOI: https://doi.org/10.1073/pnas.1914677117
Code/Server: https://yanglab.qd.sdu.edu.cn/trRosetta/
AlphaFold2
Date: 15-Jul-21
Target: Proteins
Paper: Highly accurate protein structure prediction with AlphaFold
DOI: https://doi.org/10.1038/s41586-021-03819-2
Code/Server: https://github.com/google-deepmind/alphafold3
RosettaFold
Date: 19-Aug-21
Target: Proteins
Paper: Accurate prediction of protein structures and interactions using a three-track neural network
DOI: https://doi.org/10.1126/science.abj8754
Code/Server: https://github.com/RosettaCommons/RoseTTAFold
DeepfoldRNA
Date: 15-May-22
Target: RNA 3D
Paper: De Novo?RNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning
DOI: https://doi.org/10.1101/2022.05.15.491755
Code/Server: https://github.com/robpearc/DeepFoldRNA
DeepPotential
Date: 18-May-22
Target: Proteins
Paper: Deep learning geometrical potential for high-accuracy ab initio protein structure prediction
DOI: https://doi.org/10.1016/j.isci.2022.104425
Code/Server: https://zhanggroup.org/DeepPotential/
OmegaFold
Date: 20-Jul-22
Target: Proteins
Paper: High-resolution de novo structure prediction from primary sequence
DOI: https://doi.org/10.1101/2022.07.21.500999
Code/Server: https://github.com/HeliXonProtein/OmegaFold
EquiFold
Date: 2-Jan-23
Target: Proteins
Paper: EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
DOI: https://doi.org/10.1101/2022.10.07.511322
Code/Server: https://github.com/Genentech/equifold
EigenFold
Date: 5-Apr-23
Target: Proteins
Paper: EigenFold: Generative Protein Structure Prediction with Diffusion Models
DOI: https://doi.org/10.48550/arXiv.2304.02198
Code/Server: https://github.com/bjing2016/EigenFold
DiffPack
Date: 15-Jun-23
Target: Proteins
Paper: DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
DOI: https://proceedings.neurips.cc/paper_files/paper/2023/file/96a54c09569ebbdd9ecb22f5012e6b66-Paper-Conference.pdf
Code/Server: https://github.com/DeepGraphLearning/DiffPack
HelixFold
Date: 9-Sep-23
Target: Proteins
Paper: A method for multiple-sequence-alignment-free protein structure prediction using a protein language model
DOI: https://doi.org/10.1038/s42256-023-00721-6
Code/Server: https://github.com/PaddlePaddle/PaddleHelix
DRfold
Date: 16-Sep-23
Target: RNA 3D
Paper: Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
DOI: https://doi.org/10.1038/s41467-023-41303-9
Code/Server: https://github.com/leeyang/DRfold/
DiAMoNDBack
Date: 31-Oct-23
Target: Proteins
Paper: DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of C? Protein Traces
DOI: https://doi.org/10.1021/acs.jctc.3c00840
Code/Server: https://github.com/Ferg-Lab/DiAMoNDBack
trRosettaRNA
Date: 9-Nov-23
Target: RNA
Paper: trRosettaRNA: automated prediction of RNA 3D structure with transformer network
DOI: https://doi.org/10.1038/s41467-023-42528-4
Code/Server: https://yanglab.qd.sdu.edu.cn/trRosettaRNA/
RoseTTAFoldNA
Date: 23-Nov-23
Target: Protein-nucleic acids
Paper: Accurate prediction of protein?nucleic acid complexes using RoseTTAFoldNA
DOI: https://www.nature.com/articles/s41592-023-02086-5
Code/Server: https://github.com/uw-ipd/RoseTTAFold2NA
Deepfold
Date: 23-Nov-23
Target: Proteins
Paper: DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
DOI: https://doi.org/10.1093/bioinformatics/btad712
Code/Server: https://github.com/newtonjoo/deepfold
ConfSolv
Date: 15-Dec-23
Target: Small molecules
Paper: ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents
DOI: https://doi.org/10.1021/acs.jpcb.3c05904
Code/Server: https://github.com/PattanaikL/conf_solv
RosettaFold-AA
Date: 7-Mar-24
Target: All atoms
Paper: Generalized biomolecular modeling and design with RoseTTAFold All-Atom
DOI: https://doi.org/10.1126/science.adl2528
Code/Server: https://github.com/baker-laboratory/RoseTTAFold-All-Atom
AF3
Date: 8-May-24
Target: All atoms
Paper: Accurate structure prediction of biomolecular interactions with AlphaFold 3
DOI: https://doi.org/10.1038/s41586-024-07487-w
Code/Server: https://github.com/google-deepmind/alphafold3
OpenFold
Date: 14-May-24
Target: Proteins
Paper: OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
DOI: https://doi.org/10.1038/s41592-024-02272-z
Code/Server: https://github.com/aqlaboratory/openfold
HelixFold3
Date: 30-Aug-24
Target: All atoms
Paper: Technical Report of HelixFold3 for Biomolecular Structure Prediction
DOI: https://doi.org/10.48550/arXiv.2408.16975
Code/Server: https://paddlehelix.baidu.com/app/all/helixfold3/forecast
Chai
Date: 15-Oct-24
Target: All atoms
Paper: Chai-1: Decoding the molecular interactions of life
DOI: https://doi.org/10.1101/2024.10.10.615955
Code/Server: https://github.com/chaidiscovery/chai-lab/
RhoFold+
Date: 21-Nov-24
Target: RNA 3D
Paper: Accurate RNA 3D structure prediction using a language model-based deep learning approach
DOI: https://doi.org/10.1038/s41592-024-02487-0
Code/Server: https://github.com/ml4bio/RhoFold
NCPepFold
Date: 9-Dec-24
Target: Cyclic peptides
Paper: NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation
DOI: https://doi.org/10.1021/acs.jctc.5c00139
Code/Server: https://github.com/mqyii/NCPepFold
CoarsenConf
Date: 17-Dec-24
Target: Small molecules
Paper: CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation
DOI: https://doi.org/10.1021/acs.jcim.4c01001
Code/Server: https://github.com/ASK-Berkeley/CoarsenConf
Boltz-1
Date: 27-Dec-24
Target: All atoms
Paper: Boltz-1: Democratizing Biomolecular Interaction Modeling
DOI: https://doi.org/10.1101/2024.11.19.624167
Code/Server: https://github.com/jwohlwend/boltz
RNA-TorsionBERT
Date: 8-Jan-25
Target: RNA 3D
Paper: RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction
DOI: https://doi.org/10.1093/bioinformatics/btaf004
Code/Server: https://github.com/EvryRNA/RNA-TorsionBERT
Protenix
Date: 11-Jan-25
Target: All atoms
Paper: Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction
DOI: https://doi.org/10.1101/2025.01.08.631967
Code/Server: https://github.com/bytedance/Protenix
HighFold2
Date: 21-Jan-25
Target: Cyclic peptides
Paper: Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2
DOI: https://doi.org/10.1101/2025.01.16.633493
Code/Server: https://github.com/hongliangduan/HighFold2
NuFold
Date: 21-Jan-25
Target: RNA 3D
Paper: NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation
DOI: https://doi.org/10.1038/s41467-025-56261-7
Code/Server: https://github.com/kiharalab/nufold/
RareFold
Date: 23-May-25
Target: Proteins with non-standard residues
Paper: RareFold: Structure prediction and design of proteins with noncanonical amino acids
DOI: https://doi.org/10.1101/2025.05.19.654846
Code/Server: https://github.com/patrickbryant1/RareFold
Boltz-2
Date: 18-Jun-25
Target: All atoms
Paper: Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction
DOI: https://doi.org/10.1101/2025.06.14.659707
Code/Server: https://github.com/jwohlwend/boltz