Search found 77 matches
- Sat Jul 27, 2024 11:53 am
- Forum: Main Forum
- Topic: US-align vs TM-align for antibody alignment
- Replies: 1
- Views: 2390
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: 3905
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: 4961
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: 60293
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: 108270
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: 108114
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: 108270
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: 61588
Re: US Align - superimposition of all proteins
No, -dir1 cannot work with -o.
- Fri Mar 15, 2024 12:17 pm
- Forum: Main Forum
- Topic: BioLip column names clarification
- Replies: 5
- Views: 74969
Re: BioLip column names clarification
If there are multiple instances of the same type of ligand in the same chain, they will be sequentially labeled as 1,2,3, ... by ligand serial number, For example, PDB 117e chain B has four copies of MN ligands, which have ligand serial number of 1, 2, 3, and 4, respectively. I am afraid you made a ...
- Wed Mar 06, 2024 5:40 pm
- Forum: Main Forum
- Topic: BioLip column names clarification
- Replies: 5
- Views: 74969
Re: BioLip column names clarification
“Binding Site Number Code” is the index of ligand binding sites. For example, PDB 10mh chain A has three ligands: two DNAs and one SAH. Their binding sites are sequentially numbered BS01, BS02, BS03, respectively.