<p>If you want to reproduce the model in that paper, you should email the corresponding author asking for the exact set of PDB IDs/chain IDs/residue ranges they used. There is too much flexibility in the criteria as given to get the exact set any other way.</p>

<p>If you want to assemble a similar set for your own work, the RCSB PDB advanced search is very powerful and would let you filter e.g. by max sequence length or for only monomers.</p>

<p>However the PDB doesn't deal with domains (regions that evolve and fold independently) directly. A PDB chain may contain part of a domain, one domain, or multiple domains.</p>

<p>If you want a dataset of protein domains you could use <a href="http://www.cathdb.info" rel="nofollow noreferrer">CATH</a>, <a href="http://scop.berkeley.edu" rel="nofollow noreferrer">SCOP</a> or <a href="http://prodata.swmed.edu/ecod" rel="nofollow noreferrer">ECOD</a>.</p>

<p>As a side issue, please remember to remove overlap of homologous proteins between the training and test sets. People entering the field often neglect to do that. See for example <a href="https://www.nature.com/articles/s41580-019-0176-5" rel="nofollow noreferrer">this comment piece</a>.</p>

CC BY-SA 4.0
2020-04-07T17:30:44.040Z
That is very helpful. Thank you for your answer.
Alexander
CC BY-SA 4.0
2020-04-07T11:12:40.630Z
2020-04-07T11:12:40.630Z
jgreener
<p>I am trying to reproduce a machine learning model that has been developed <a href="https://www.biorxiv.org/content/10.1101/842336v1" rel="nofollow noreferrer">here</a>. As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a background in biology, I am not sure how to filter the <a href="https://www.rcsb.org/" rel="nofollow noreferrer">PDB</a> for these kind of proteins. Any help would be appreciated.</p>

<proteins>
How to filter the PDB for single-domain proteins with full length 3D-structures solved
# How to filter the PDB for single-domain proteins with full length 3D-structures solved

(Asked by: username_0 on 2020-04-06)

I am trying to reproduce a machine learning model that has been developed [here](https://www.biorxiv.org/content/10.1101/842336v1). As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a background in biology, I am not sure how to filter the [PDB](https://www.rcsb.org/) for these kind of proteins. Any help would be appreciated.

**Tags:** proteins

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## 1 answers

### Answer by username_1 on 2020-04-07. Score: 3 | Accepted answer

If you want to reproduce the model in that paper, you should email the corresponding author asking for the exact set of PDB IDs/chain IDs/residue ranges they used. There is too much flexibility in the criteria as given to get the exact set any other way.

If you want to assemble a similar set for your own work, the RCSB PDB advanced search is very powerful and would let you filter e.g. by max sequence length or for only monomers.

However the PDB doesn't deal with domains (regions that evolve and fold independently) directly. A PDB chain may contain part of a domain, one domain, or multiple domains.

If you want a dataset of protein domains you could use [CATH](http://www.cathdb.info), [SCOP](http://scop.berkeley.edu) or [ECOD](http://prodata.swmed.edu/ecod).

As a side issue, please remember to remove overlap of homologous proteins between the training and test sets. People entering the field often neglect to do that. See for example [this comment piece](https://www.nature.com/articles/s41580-019-0176-5).

> **Comments:**
> **username_0**: That is very helpful. Thank you for your answer.  

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