<p>As suggested in the comments, PDB is the standard database for protein structural information. I would suggest starting there. They even have <a href="https://www.rcsb.org/news/5ba160306078e948d6421755" rel="nofollow noreferrer">some degree of geometric information precomputed for you</a>, there is an <a href="https://data.rcsb.org/index.html#data-api" rel="nofollow noreferrer">API / GraphQL interface</a> that can be used to query <a href="https://data.rcsb.org/data-attributes.html" rel="nofollow noreferrer">certain attributes</a> that do seem to include some geometric measurements and structural annotations.</p>
<p>You will likely have to compute some of the measures you are interested in, it seems that your list is somewhat amorphous regarding which geometric measurements you'd like to measure so I can't recommend much specifically. For very basic things like <a href="https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/ramachandran/calculate/" rel="nofollow noreferrer">Ramachandran angles there are various resources</a> you could use, though <a href="https://biopython.org/docs/dev/api/Bio.PDB.internal_coords.html" rel="nofollow noreferrer">Biopython is probably the easiest</a>.</p>
<p>There used to be a &quot;<a href="https://bio.tools/pgd" rel="nofollow noreferrer">Protein Geometry Database</a>&quot; that is now defunct, probably because it is not hard to compute this stuff directly on any given PDB file.</p>

CC BY-SA 4.0
2024-06-05T18:57:40.340Z
2024-06-05T18:57:40.340Z
Maximilian Press
<p>I want to do ML model training and data analysis for secondary structure prediction.</p>
<p>Is there any standardized and ready-to-use dataset available online regarding protein geometry?</p>
<p>For example, the dataset should have common features like: distances, angles, dihedrals, etc.</p>

CC BY-SA 4.0
2024-05-31T08:08:37.930Z
I'm confused as to what you are looking for - any data with 2 points will have a distance, and three points will have an angle. Do you mean protein data with the distances, angles, and dihedrals labelled? Why not use a library/tool to calculate these measurements on a dataset?
gilleain
CC BY-SA 4.0
2024-06-01T02:54:12.033Z
Your question is not verbose enough to be helpful. What is the specific project and/or problem that you are trying to solve with this? General questions and answers in bioinformatics are rarely helpful to anyone; see https://bioinformatics.stackexchange.com/help/on-topic
gringer
CC BY-SA 4.0
2024-06-01T06:57:04.413Z
@gringer, *What is the specific project and/or problem that you are trying to solve with this?* --- Secondary structure prediction.
user366312
CC BY-SA 4.0
2024-06-01T13:39:18.340Z
@user366312 please ***edit*** and give more details. [Secondary structure prediction](https://en.wikipedia.org/wiki/Protein_secondary_structure#Prediction) is not that hard, did you mean _tertiary_ structure? And what exact type of data would you want and what kind of predictions would you be making? Have you read through the SwissModel, or AlphaFold papers? Their references? Are you just looking for [Pfam](https://www.ebi.ac.uk/interpro/entry/pfam/#table)? Or maybe [RCSB PDB](https://www.rcsb.org/)? We can't help if you don't explain.
terdon
CC BY-SA 4.0
2024-06-06T19:47:53.077Z
I'm closing this question because it is a general question that is not sufficiently described to give good / useful answers. Please edit to add more details, or ask this question on a discussion site like [Reddit](https://reddit.com/r/bioinformatics)
gringer
<proteins><protein-structure><public-dataset>
Is there any standardized and ready-to-use dataset available online for download regarding protein geometry?
# Is there any standardized and ready-to-use dataset available online for download regarding protein geometry?

(Asked by: username_0 on 2024-05-30)

I want to do ML model training and data analysis for secondary structure prediction.

Is there any standardized and ready-to-use dataset available online regarding protein geometry?

For example, the dataset should have common features like: distances, angles, dihedrals, etc.

**Tags:** proteins, protein-structure, public-dataset
> **Comments:**
> **username_1**: I'm confused as to what you are looking for - any data with 2 points will have a distance, and three points will have an angle. Do you mean protein data with the distances, angles, and dihedrals labelled? Why not use a library/tool to calculate these measurements on a dataset?  
> **username_2**: Your question is not verbose enough to be helpful. What is the specific project and/or problem that you are trying to solve with this? General questions and answers in bioinformatics are rarely helpful to anyone; see https://bioinformatics.stackexchange.com/help/on-topic  
> **username_0**: @gringer, *What is the specific project and/or problem that you are trying to solve with this?* --- Secondary structure prediction.  
> **username_3**: @user366312 please ***edit*** and give more details. [Secondary structure prediction](https://en.wikipedia.org/wiki/Protein_secondary_structure#Prediction) is not that hard, did you mean _tertiary_ structure? And what exact type of data would you want and what kind of predictions would you be making? Have you read through the SwissModel, or AlphaFold papers? Their references? Are you just looking for [Pfam](https://www.ebi.ac.uk/interpro/entry/pfam/#table)? Or maybe [RCSB PDB](https://www.rcsb.org/)? We can't help if you don't explain.  
> **username_2**: I'm closing this question because it is a general question that is not sufficiently described to give good / useful answers. Please edit to add more details, or ask this question on a discussion site like [Reddit](https://reddit.com/r/bioinformatics)  

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## 1 answers

### Answer by username_4 on 2024-06-05. Score: 1

As suggested in the comments, PDB is the standard database for protein structural information. I would suggest starting there. They even have [some degree of geometric information precomputed for you](https://www.rcsb.org/news/5ba160306078e948d6421755), there is an [API / GraphQL interface](https://data.rcsb.org/index.html#data-api) that can be used to query [certain attributes](https://data.rcsb.org/data-attributes.html) that do seem to include some geometric measurements and structural annotations.

You will likely have to compute some of the measures you are interested in, it seems that your list is somewhat amorphous regarding which geometric measurements you'd like to measure so I can't recommend much specifically. For very basic things like [Ramachandran angles there are various resources](https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/ramachandran/calculate/) you could use, though [Biopython is probably the easiest](https://biopython.org/docs/dev/api/Bio.PDB.internal_coords.html).

There used to be a "[Protein Geometry Database](https://bio.tools/pgd)" that is now defunct, probably because it is not hard to compute this stuff directly on any given PDB file.


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