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Title: Using RFdiffusion — OpenProtein-Docs documentation

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Designing sequenceshttps://docs.openprotein.ai/python-api/property-regression-models/designing-sequences.html
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Structure Predictionhttps://docs.openprotein.ai/python-api/structure-prediction/index.html
Examining structure prediction modelshttps://docs.openprotein.ai/python-api/structure-prediction/Examining_structure_prediction_models.html
Using ESMFold2https://docs.openprotein.ai/python-api/structure-prediction/Using_ESMFold2.html
Using AlphaFold2https://docs.openprotein.ai/python-api/structure-prediction/Using_AlphaFold2.html
Using Boltz-1 and Boltz-2https://docs.openprotein.ai/python-api/structure-prediction/Using_Boltz_1_and_Boltz_2.html
Using Protenix-v2https://docs.openprotein.ai/python-api/structure-prediction/Using_Protenix-v2.html
Using RosettaFold-3https://docs.openprotein.ai/python-api/structure-prediction/Using_RosettaFold3.html
Structure Generationhttps://docs.openprotein.ai/python-api/structure-generation/index.html
Using RFdiffusionhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html
Using BoltzGenhttps://docs.openprotein.ai/python-api/structure-generation/Using_BoltzGen.html
API referencehttps://docs.openprotein.ai/python-api/api-reference/index.html
openproteinhttps://docs.openprotein.ai/python-api/api-reference/openprotein.html
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openprotein.designhttps://docs.openprotein.ai/python-api/api-reference/design.html
openprotein.foldhttps://docs.openprotein.ai/python-api/api-reference/fold.html
openprotein.modelshttps://docs.openprotein.ai/python-api/api-reference/models.html
https://docs.openprotein.ai/index.html
Python API Documentationhttps://docs.openprotein.ai/python-api/index.html
Structure Generationhttps://docs.openprotein.ai/python-api/structure-generation/index.html
https://colab.research.google.com/github/OpenProteinAI/openprotein-docs/blob/main/source/python-api/structure-generation/Using_RFdiffusion.ipynb
https://raw.githubusercontent.com/OpenProteinAI/openprotein-docs/refs/heads/main/source/python-api/structure-generation/Using_RFdiffusion.ipynb
https://github.com/OpenProteinAI/openprotein-docs/blob/main/source/python-api/structure-generation/Using_RFdiffusion.ipynb
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Using-RFdiffusion
original documentationhttps://github.com/RosettaCommons/RFdiffusion
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Unconditional-monomer-design
Protein.from_exprhttps://docs.openprotein.ai/python-api/api-reference/molecules.html#openprotein.molecules.Protein.from_expr
Complexhttps://docs.openprotein.ai/python-api/api-reference/molecules.html#openprotein.molecules.Complex
ProteinMPNNhttps://docs.openprotein.ai/python-api/api-reference/models.html#openprotein.models.ProteinMPNNModel
binder designhttps://docs.openprotein.ai/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.html
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Motif-Scaffolding
crystal structure of RSV F in complex with human antibody hRSV90https://www.rcsb.org/structure/5TPN
Structure.from_pdb_idhttps://docs.openprotein.ai/python-api/api-reference/molecules.html#openprotein.molecules.Structure.from_pdb_id
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Small-motifs-using-active-site-model
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Binder-design
Practical Considerations for Binder Designhttps://github.com/RosettaCommons/RFdiffusion?tab=readme-ov-file#practical-considerations-for-binder-design
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Higher-diversity-topologies-using-complex-beta-model
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Next-Steps
using BoltzGenhttps://docs.openprotein.ai/python-api/structure-generation/Using_BoltzGen.html
Binder Design with RFdiffusionhttps://docs.openprotein.ai/walkthroughs/Protein_protein_binder_design_with_RFdiffusion.html
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Appendix:-Low-level-RFdiffusion
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Partial-diffusion
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Keeping-some-sequences
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Fold-conditioning
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Binder-design-to-flexible-peptides
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Generating-symmetric-oligomers
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Cyclic
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Dihedral
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Tetrahedral
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Symmetric-motif-scaffolding
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Macrocyclic-peptide-design-with-RFpeptides
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Macrocyclic-binder-design
#https://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Macrocyclic-monomer-design
Using RFdiffusionhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html
Unconditional monomer designhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Unconditional-monomer-design
Motif Scaffoldinghttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Motif-Scaffolding
Small motifs using active site modelhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Small-motifs-using-active-site-model
Binder designhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Binder-design
Higher diversity topologies using complex beta modelhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Higher-diversity-topologies-using-complex-beta-model
Next Stepshttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Next-Steps
Appendix: Low-level RFdiffusionhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Appendix:-Low-level-RFdiffusion
Partial diffusionhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Partial-diffusion
Keeping some sequenceshttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Keeping-some-sequences
Fold conditioninghttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Fold-conditioning
Binder design to flexible peptideshttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Binder-design-to-flexible-peptides
Generating symmetric oligomershttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Generating-symmetric-oligomers
Cyclichttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Cyclic
Dihedralhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Dihedral
Tetrahedralhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Tetrahedral
Symmetric motif scaffoldinghttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Symmetric-motif-scaffolding
Macrocyclic peptide design with RFpeptideshttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Macrocyclic-peptide-design-with-RFpeptides
Macrocyclic binder designhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Macrocyclic-binder-design
Macrocyclic monomer designhttps://docs.openprotein.ai/python-api/structure-generation/Using_RFdiffusion.html#Macrocyclic-monomer-design
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