Search found 76 matches

by zcx@umich.edu
Wed Oct 09, 2024 1:59 am
Forum: Main Forum
Topic: BioLip data
Replies: 1
Views: 3460

Re: BioLip data

You may check https://zhanggroup.org/BioLiP/download.html
which contains "BioLiP.txt.gz".
by zcx@umich.edu
Wed Oct 09, 2024 1:57 am
Forum: Main Forum
Topic: the two TM-scores from US-align show a large discrepancy
Replies: 4
Views: 3404

Re: the two TM-scores from US-align show a large discrepancy

This is not a problem of US-align. You are using the incorrect file for 1ha0. While it is true that 1ha0 is a homotrimer, each asymmetric unit of 1ha0 only contain one chain. 1ha0.cif.gz is the asymmetric file, which contains and only contains one chain. You can check this by any molecular graphic s...
by zcx@umich.edu
Sat Jul 27, 2024 11:53 am
Forum: Main Forum
Topic: US-align vs TM-align for antibody alignment
Replies: 1
Views: 5828

Re: US-align vs TM-align for antibody alignment

If you are aligning monomeric proteins, TM-align and US-align give the same result.
by zcx@umich.edu
Tue Jul 09, 2024 6:49 pm
Forum: Main Forum
Topic: How to compare multiple protein structures with TM-align
Replies: 1
Views: 6568

Re: How to compare multiple protein structures with TM-align

AlphaFold structures of all human proteins can be downloaded via the alphafold database https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000005640_9606_HUMAN_v4.tar You can then perform pairwise TM-align alignments. You probably would want to use the "-fast" option of the TM-align (C...
by zcx@umich.edu
Thu Jun 27, 2024 11:17 am
Forum: Main Forum
Topic: USalign RMSD
Replies: 1
Views: 6482

Re: USalign RMSD

To calculate the RMSD, a Kabsch superimposition (a.k.a. RMSD superimposition) is performed on the subset of aligned residue pairs and the RMSD can be calculated by: RMSD = sqrt ( 1/Lali \sum_{i=1}^Lali d_i ^2 ) where Lali is the number of aligned residue pairs, d_i is the distance between the i-th a...
by zcx@umich.edu
Thu May 02, 2024 7:34 pm
Forum: Main Forum
Topic: Biolip: pocket - chain relationship
Replies: 2
Views: 62177

Re: Biolip: pocket - chain relationship

8stw is a homo-hexamer, where each chain binds to one PLP and one HEM. Therefore, the full biological assembly has 6 different PLP and 6 different HEM ligands for the 6 different chains. Therefore, it is not true that the same ligand binds to 6 different chains simultaneously.
by zcx@umich.edu
Thu May 02, 2024 7:21 pm
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 112206

Re: Restricting TM-align to a given superposition

I am afraid what you request is not implementable. It is not possible to implement rotation but no translation.
by zcx@umich.edu
Thu May 02, 2024 7:11 pm
Forum: Main Forum
Topic: Alignment based on pLDDT
Replies: 1
Views: 109465

Re: Alignment based on pLDDT

No, US-align cannot consider pLDDT score.
by zcx@umich.edu
Tue Apr 16, 2024 8:15 am
Forum: Main Forum
Topic: Restricting TM-align to a given superposition
Replies: 4
Views: 112206

Re: Restricting TM-align to a given superposition

I am not exactly sure what you mean. If you want to extract the alignment based on a pair of superimposed structure, you can use the "se" program from https://github.com/pylelab/USalign
by zcx@umich.edu
Tue Apr 16, 2024 8:13 am
Forum: Main Forum
Topic: US Align - superimposition of all proteins
Replies: 3
Views: 64288

Re: US Align - superimposition of all proteins

No, -dir1 cannot work with -o.