You may check https://zhanggroup.org/BioLiP/download.html
which contains "BioLiP.txt.gz".
Search found 76 matches
- Wed Oct 09, 2024 1:59 am
- Forum: Main Forum
- Topic: BioLip data
- Replies: 1
- Views: 3462
- 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...
- 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.
- 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...
- 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...
- 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.
- 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.
- 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.
- 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
- 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.