Multi Chain alignement ?

pylelab / USalign

Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins

https://zhanggroup.org/US-align/

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Multi Chain alignement ? #23

Closed PodevynLoris closed 10 months ago

PodevynLoris commented 10 months ago

Does US-align support the alignment of a monomer to a multi-chain protein complex while considering the spatial relationship between the chains in the complex? For example, I have a monomer that I'm trying to align to an antibody fragment composed of two chains. Could you provide any examples or documentation on how to conduct such alignments using US-align

kad-ecoli commented 10 months ago

The recommended flag for your purpose is

USalign -mm 1 monomer.pdb complex.pdb -ter 0

This will align the monomer to the most similar chain in the complex.