ProtStruc

What is ProtStruc?

ProtStruc is a Python package for handling protein structures, especially for deep learning applications, through a simple, flexible, and efficient representation of protein structures.

There are many ways to represent protein structures in various deep learning applications:

Year & Source	Category	Deep learning application	Protein structure representation
2020, PNAS	Structure prediction	TrRoseTTA	Inter-residue geometry
2021, Science	Structure prediction	RoseTTAFold	Inter-residue geometry
2021, Nature	Structure prediction	AlphaFold2	Orientation & translation of backbone frames centered at Ca's
2022, Patterns	Structure prediction	DeepAb	Inter-residue geometry
2023, Nat. Commun.	Antibody structure prediction	IgFold	Oritentation & translation of backbone frames centered at Ca's
2022, arXiv	Structure generation	FoldingDiff	Three backbone dihedrals and three bond angles
2022, NeurIPS	Structure generation	DiffAb	Orientation & translation of backbone frames centered at Ca's
2022, Science	Inverse-folding	ProteinMPNN	k-nearest neighbor graph
2022, arXiv	Inverse-folding	PiFold	Inter-atomic/residue distance, backbone dihedrals and bond angles, orientation of residue frame, inter-residue orientations
2023, Science	Structure prediction	ESMFold	Orientation & translation of backbone frames centered at Ca's
2023, ICML	Structure generation	FrameDiff	Orientation & translation of backbone frames centered at Ca's, an additional torsion angle for oxygen atom
2022, ICML	Structure generation	Hierarchical Equivariant Refinement Network (HERN)
2022, arXiv	Sequence-structure co-design	Multi-channel Equivariant Attention Network (MEAN)
2023, ICML	Sequence-structure co-design	Dynamic multi-channel Equivariant Attention Network (dyMEAN)