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pylelab / USalign

Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins
https://zhanggroup.org/US-align/
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-fast option with multimer alignment #16

Closed mrauha closed 1 year ago

mrauha commented 1 year ago

Hi,

In Supplementary Figure 9, it is demonstrated that fTM-align significantly speeds up the alignment of larger structures. However, using the -fast flag for multimer alignment has no effect on the calculation time or the alignment results. Below is the code to replicate this, I'm using the current version of US-align from this repository.

wget https://files.rcsb.org/download/7NYH.cif
wget https://files.rcsb.org/download/7NYU.cif
time ./USalign 7NYU.cif 7NYH.cif -mm 1 -ter 0 -fast | head -16 | tail -3
time ./USalign 7NYU.cif 7NYH.cif -mm 1 -ter 0 | head -16 | tail -3

gives 

# fTM-align
Aligned length= 2195, RMSD=   0.83, Seq_ID=n_identical/n_aligned= 1.000
TM-score= 0.47471 (normalized by length of Structure_1: L=4615, d0=18.82)
TM-score= 0.99666 (normalized by length of Structure_2: L=2195, d0=14.28)

real    0m12.052s

# TM-align
Aligned length= 2195, RMSD=   0.83, Seq_ID=n_identical/n_aligned= 1.000
TM-score= 0.47471 (normalized by length of Structure_1: L=4615, d0=18.82)
TM-score= 0.99666 (normalized by length of Structure_2: L=2195, d0=14.28)

real    0m12.052s

Is there a reason why fTM-align doesn't work for multimers?

Thanks!

kad-ecoli commented 1 year ago

-fast is always turned on for -mm 1 if the length of the smaller complex is greater than 500 residues. This is implemented by line 645 of https://github.com/pylelab/USalign/blob/master/USalign.cpp