<p>Did you try RCSB <a href="https://www4.rcsb.org/search/advanced/sequence" rel="nofollow noreferrer">sequence similarity search</a>?
These two announcement highlight the options you ask about:</p>
<ul>
<li><a href="https://www.rcsb.org/news/5764422199cccf72e74ca34f" rel="nofollow noreferrer">Improved Searching with New Sequence Identity Cutoff</a> (2017)</li>
<li><a href="https://www.rcsb.org/news/feature/61b8e5e869569d045d35a9a3" rel="nofollow noreferrer">Remove Redundancy in Search Results</a> (2015)</li>
</ul>
<p>Alternatively, if you'd like to calculate identity on your own, you can download sequences of all the PDB entries from:
<a href="https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt" rel="nofollow noreferrer">https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt</a>
(270MB).</p>

CC BY-SA 4.0
2023-11-06T01:27:46.410Z
Thank you!  The https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt link was what I needed.  Any way to filter them by identity from the text file?
user18494
CC BY-SA 4.0
2023-11-06T07:03:51.060Z
I suppose you'd need to do pairwise sequence alignment and calculate identity.
marcin
CC BY-SA 4.0
2023-11-05T13:47:07.143Z
2023-11-05T13:47:07.143Z
marcin
<p>I'm trying to download a list of all of the non-redundant protein chain IDs in the RSCB-PDB (not the actual FASTA entries, just the IDs), filtered by some % identity.</p>
<p>Does anyone know how to do this?  I haven't been able to figure it out with the <a href="https://www.rcsb.org/search" rel="nofollow noreferrer">advanced search function</a> .</p>

CC BY-SA 4.0
2023-11-04T20:27:20.597Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2023-11-05T11:15:27.833Z
% identity to what? To each other? To a specific query sequence?
terdon
CC BY-SA 4.0
2023-11-05T11:18:14.107Z
Please add some additional context to your question. Why dod you want to download this list?
gringer
CC BY-SA 4.0
2023-11-05T12:11:37.617Z
@terdon I believe he needs the ones not identical AKA different ones ' non-redundant' as he says
pippo1980
CC BY-SA 4.0
2023-11-05T12:24:30.887Z
So the ones that do not have more than X% identity to any others in the database, @pippo1980? OK, so what identity? And won't _all_ of them be non-redundant? I mean, if they are identical, they wouldn't have a different ID, would they? (I know, my deep, deep ignorance of the protein structure field is probably evident here)
terdon
CC BY-SA 4.0
2023-11-05T12:31:33.180Z
@terdon I dont know a lot about it either but I guess you are right the OP should specify a number and whath the number stands for it coukd be both sequence identity or structure identity but probably for the latter we are talking about mainchain Root Mean Square Deviation (RMSD),
pippo1980
CC BY-SA 4.0
2023-11-05T12:48:39.153Z
but maybe is just this : https://www.rcsb.org/news/feature/61b8e5e869569d045d35a9a3 Remove Redundancy in Search Results
pippo1980
CC BY-SA 4.0
2023-11-05T12:52:15.857Z
@terdon I'm a computational biologist with a background in biology, not computers. I did my PhD work on gene prediction and comparative evolution, my post-doc on protein-protein interaction networks and I have been working in NGS analysis, specifically human variant calling and annotation, for the past several years. Jack of many trades and master of none. .. I know, my deep, deep ignorance of the protein structure field is probably evident here ... YES SURE .... ;-)
pippo1980
<proteins><protein-structure><pdb>
Downloading a list of all RCSB-PDB entries
# Downloading a list of all RCSB-PDB entries

(Asked by: username_0 on 2023-11-04)

I'm trying to download a list of all of the non-redundant protein chain IDs in the RSCB-PDB (not the actual FASTA entries, just the IDs), filtered by some % identity.

Does anyone know how to do this? I haven't been able to figure it out with the [advanced search function](https://www.rcsb.org/search) .

**Tags:** proteins, protein-structure, pdb
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: % identity to what? To each other? To a specific query sequence?  
> **username_3**: Please add some additional context to your question. Why dod you want to download this list?  
> **username_4**: @terdon I believe he needs the ones not identical AKA different ones ' non-redundant' as he says  
> **username_2**: So the ones that do not have more than X% identity to any others in the database, @pippo1980? OK, so what identity? And won't _all_ of them be non-redundant? I mean, if they are identical, they wouldn't have a different ID, would they? (I know, my deep, deep ignorance of the protein structure field is probably evident here)  
> **username_4**: @terdon I dont know a lot about it either but I guess you are right the OP should specify a number and whath the number stands for it coukd be both sequence identity or structure identity but probably for the latter we are talking about mainchain Root Mean Square Deviation (RMSD),  
> **username_4**: but maybe is just this : https://www.rcsb.org/news/feature/61b8e5e869569d045d35a9a3 Remove Redundancy in Search Results  
> **username_4**: @terdon I'm a computational biologist with a background in biology, not computers. I did my PhD work on gene prediction and comparative evolution, my post-doc on protein-protein interaction networks and I have been working in NGS analysis, specifically human variant calling and annotation, for the past several years. Jack of many trades and master of none. .. I know, my deep, deep ignorance of the protein structure field is probably evident here ... YES SURE .... ;-)  

---

## 1 answers

### Answer by username_5 on 2023-11-05. Score: 1

Did you try RCSB [sequence similarity search](https://www4.rcsb.org/search/advanced/sequence)?
These two announcement highlight the options you ask about:

* [Improved Searching with New Sequence Identity Cutoff](https://www.rcsb.org/news/5764422199cccf72e74ca34f) (2017)
* [Remove Redundancy in Search Results](https://www.rcsb.org/news/feature/61b8e5e869569d045d35a9a3) (2015)

Alternatively, if you'd like to calculate identity on your own, you can download sequences of all the PDB entries from:
<https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt>
(270MB).

> **Comments:**
> **username_0**: Thank you!  The https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt link was what I needed.  Any way to filter them by identity from the text file?  
> **username_5**: I suppose you'd need to do pairwise sequence alignment and calculate identity.  

---

