Structure Prediction Tools

Date	Name	Title	Target	Code/Server
15-Jul-21	AlphaFold2	Highly accurate protein structure prediction with AlphaFold	Proteins	Link
8-May-24	AlphaFold3	Accurate structure prediction of biomolecular interactions with AlphaFold 3	All atoms	Link
27-Dec-24	Boltz-1	Boltz-1: Democratizing Biomolecular Interaction Modeling	All atoms	Link
18-Jun-25	Boltz-2	Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction	All atoms	Link
15-Oct-24	Chai	Chai-1: Decoding the molecular interactions of life	All atoms	Link
17-Dec-24	CoarsenConf	CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation	Small molecules	Link
15-Dec-23	ConfSolv	ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents	Small molecules	Link
23-Nov-23	Deepfold	DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function	Proteins	Link
15-May-22	DeepfoldRNA	De Novo?RNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning	RNA 3D	Link
18-May-22	DeepPotential	Deep learning geometrical potential for high-accuracy ab initio protein structure prediction	Proteins	Link
31-Oct-23	DiAMoNDBack	DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces	Proteins	Link
15-Jun-23	DiffPack	DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing	Proteins	Link
16-Sep-23	DRfold	Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction	RNA 3D	Link
5-Apr-23	EigenFold	EigenFold: Generative Protein Structure Prediction with Diffusion Models	Proteins	Link
2-Jan-23	EquiFold	EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation	Proteins	Link
9-Sep-23	HelixFold	A method for multiple-sequence-alignment-free protein structure prediction using a protein language model	Proteins	Link
30-Aug-24	HelixFold3	Technical Report of HelixFold3 for Biomolecular Structure Prediction	All atoms	Link
21-Jan-25	HighFold2	Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2	Cyclic peptides	Link
9-Dec-24	NCPepFold	NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation	Cyclic peptides	Link
21-Jan-25	NuFold	NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation	RNA 3D	Link
20-Jul-22	OmegaFold	High-resolution de novo structure prediction from primary sequence	Proteins	Link
14-May-24	OpenFold	OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization	Proteins	Link
11-Jan-25	Protenix	Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction	All atoms	Link
23-May-25	RareFold	RareFold: Structure prediction and design of proteins with noncanonical amino acids	Proteins	Link
21-Nov-24	RhoFold+	Accurate RNA 3D structure prediction using a language model-based deep learning approach	RNA 3D	Link
8-Jan-25	RNA-TorsionBERT	RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction	RNA 3D	Link
19-Aug-21	RosettaFold	Accurate prediction of protein structures and interactions using a three-track neural network	Proteins	Link
7-Mar-24	RosettaFold-AA	Generalized biomolecular modeling and design with RoseTTAFold All-Atom	All atoms	Link
23-Nov-23	RoseTTAFoldNA	Accurate prediction of protein?nucleic acid complexes using RoseTTAFoldNA	Protein-nucleic acids	Link
2-Jan-20	trRosetta	Improved protein structure prediction using predicted interresidue orientations	Proteins	Link
9-Nov-23	trRosettaRNA	trRosettaRNA: automated prediction of RNA 3D structure with transformer network	RNA	Link