WebChemistry Wiki - User contributions [en]

SecStrAnnotator:Download

2022-05-17T14:11:24Z

Midlik:

'''Releases:'''

[https://gitlab.com/midlik/SecStrAnnot2/uploads/2c9b5401da4639b512793713d28be21a/SecStrAnnotator_2.3-release.zip '''SecStrAnnotator 2.3'''] (.NET 6.0 application)

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.2-release.zip SecStrAnnotator 2.2]

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.1.zip SecStrAnnotator 2.1]

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.0.zip SecStrAnnotator 2.0] (.NET Core 3.0 application, runs on CIF files)

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_1.0.zip SecStrAnnotator 1.0] (.NET Framework/Mono application, runs on PDB files)

'''Source code:'''

[https://gitlab.com/midlik/SecStrAnnot2 SecStrAnnotator on GitLab]

'''Precomputed annotations:'''

[https://webchem.ncbr.muni.cz/API/SecStr SecStrAPI]

 
----

[[SecStrAnnotator:UserManual | Back to the main page]]

SecStrAnnotator:OneToOne

2022-05-17T13:59:06Z

Midlik:

This page is about '''SecStrAnnotator 2.3''' (the page for SecStrAnnotator 1.0 is [[SecStrAnnotator:OneToOne_v1.0 | here]]).

SecStrAnnotator finds annotation for a query protein ''Q'', based on the template protein ''T''. Thus, the input consists of the structure of ''T'', structure of ''Q'', and annotation of ''T''.

Sometimes a single protein consists of several domains. In such cases, ''T'' and ''Q'' do not refer to the whole protein but only to one domain.

The annotation algorithm consists of three major steps. The first step is '''structural alignment and superimposition''' of the query protein with the template protein, so the corresponding parts of the two proteins are located close to each other. In the second step, '''secondary structure assignment (SSA)''' is performed – SSEs are detected in the query protein ''Q''. The third step is called '''matching''' – the algorithm will match the template SSEs to the query SSEs and for each annotated SSE in ''T'' it will select the corresponding SSE in ''Q''.

==Dependencies==

===.NET 6.0 runtime===

Download and install from the official [https://dotnet.microsoft.com/ .NET website]. (For SecStrAnnotator 2.0–2.2, use .NET Core 3.0 or .NET Core 3.1)

===PyMOL===

PyMOL is used by SecStrAnnotator for structural alignment and visualization. It can be downloaded from the [https://pymol.org/2/ PyMOL website]. In Ubuntu Linux it can also be installed by running <code>sudo apt install pymol</code>.

===(DSSP)===

Only needed if using DSSP secondary structure assignment method (<code>--ssa dssp</code>). In Ubuntu Linux it can be installed by running <code>sudo apt install dssp</code>.

==Execution==

SecStrAnnotator is executed from command line:

dotnet SecStrAnnotator.dll [OPTIONS] DIRECTORY TEMPLATE QUERY

Example of a call:

<source lang="bash">
dotnet SecStrAnnotator.dll --help # Show help

dotnet SecStrAnnotator.dll --onlyssa my_data_directory 1tqn,A,7:478 # Only detect SSEs

dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478 # Detect and annotate SSEs

dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478 --align cealign --matching mom --session # Detect and annotate SSEs
</source>

===Arguments===

* <code>DIRECTORY</code> is the directory containing all the input files. The output files will also be saved to this directory.
* <code>TEMPLATE</code> describes the template protein domain in one of the following formats: <code>PDB</code> or <code>PDB,CHAIN</code> or <code>PDB,CHAIN,RANGES</code>. The whole argument must be written without spaces. Examples:
** <code>1og2</code> (structure 1og2, chain A by default)
** <code>1og2,B</code> (chain B)
** <code>1og2,B,100:400</code> (residues 100–400 of the chain B)
** <code>1og2,B,:400</code> (residues up to 400 of the chain B)
** <code>1h9r,A,123:183,252:261</code> (residues 123–183 and 252–261 of the chain A)
* <code>QUERY</code> describes the query protein domain and uses the same format as <code>TEMPLATE</code>.

Keep in mind that the chains and residues are numbered according to the label_* numbering scheme in mmCIF file format (i.e. chain identifier is <code>label_asym_id</code>, residue number is <code>label_seq_id</code>).

===Options===

There is a range of options which can be used to modify the behaviour of SecStrAnnotator. The most important option is:
* <code>--help</code> Prints the help message, which includes the description of all the other options.

===Input files===

* <code>DIRECTORY/TEMPLATEPDB.cif</code> – structure of the template protein
* <code>DIRECTORY/TEMPLATEPDB-template.sses.json</code> – annotation of the template domain
* <code>DIRECTORY/QUERYPDB.cif</code> – structure of the query protein

===Output files===

* <code>DIRECTORY/QUERYPDB-aligned.cif</code> – structure of the query protein after superimposition on the template protein
* <code>DIRECTORY/QUERYPDB-detected.sses.json</code> – secondary structure assignment of the query protein, i.e. all detected SSEs
* <code>DIRECTORY/QUERYPDB-annotated.sses.json</code> – annotated SSEs in the query protein
* <code>DIRECTORY/QUERYPDB-annotated.pse</code> – PyMOL session with the visualization of the resulting annotation (only when executed with <code>--session</code> option)
* Additional output files and more detailed .sses.json files are produced when executed with <code>--verbose</code> option

===Auxiliary files and programs===

SecStrAnnotator has dependencies on other programs (PyMOL, optionally DSSP) and scripts. These auxiliary files need to be available in the system, and there location must be specified in the configuration file <code>SecStrAnnotator_config.json</code>. The configuration file itself must be in the same directory as <code>SecStrAnnotator.dll</code>. The default content of the configuration file is:
<source lang="json>
{
"PymolExecutable": "pymol",
"PymolScriptAlign": "./scripts/script_align.py",
"PymolScriptSession": "./scripts/script_session.py",
"DsspExecutable": "mkdssp"
}
</source>

which assumes that <code>pymol</code> is installed and can be run directly (from <code>$PATH</code>) and that the other files are present in subdirectory <code>scripts</code>.

On Windows, you must find the location of PyMOL executable and insert it into the configuration file.

* It will be probably some impossible-to-find file like <code>C:\Program Files\PyMOL\PyMOL\PyMOL.exe</code> or <code>C:\ProgramData\PyMOL\Scripts\pymol.exe</code> (or <code>C:/Users/Adam/miniconda3/Scripts/pymol.exe</code> if you installed PyMOL via <code>conda</code>).
* To make it more fun, <code>ProgramData</code> is a hidden directory, which is by default invisible in File Explorer.
* We're looking for PyMOL.exe, not PyMOLWin.exe. PyMOLWin.exe will run asynchronously and it will probably not work.
* Note that <code>\</code> is a special escaping character in JSON. Therefore use <code>/</code> or <code>\\</code> instead of <code>\</code>.

<source lang="json>
{
"PymolExecutable": "C:/ProgramData/PyMOL/Scripts/pymol.exe",
"PymolScriptAlign": "./scripts/script_align.py",
"PymolScriptSession": "./scripts/script_session.py",
"DsspExecutable": "./dssp.exe"
}
</source>

===Annotation file format===

All files with extension <code>.sses.json</code> are in SecStrAnnotator annotation format. A short example of this format:
<source lang="json>
{
"1tqn": {
"comment": "This is a demonstration of the annotation format. It shows a few SSEs selected from the real annotation of 1tqn.",
"secondary_structure_elements": [
{ "label": "A", "chain_id": "A", "start": 36, "end": 47, "type": "H", "sequence": "FCMFDMECHKKY" },
{ "label": "B", "chain_id": "A", "start": 66, "end": 76, "type": "h", "sequence": "PDMIKTVLVKE" },
{ "label": "1-1", "chain_id": "A", "start": 50, "end": 55, "type": "E", "sheet_id": 1, "sequence": "VWGFYD" },
{ "label": "1-2", "chain_id": "A", "start": 58, "end": 63, "type": "E", "sheet_id": 1, "sequence": "QPVLAI" },
{ "label": "1-3", "chain_id": "A", "start": 372, "end": 375, "type": "E", "sheet_id": 1, "sequence": "VVMI" }
],
"beta_connectivity": [
[ "1-1", "1-2", -1 ],
[ "1-2", "1-3", 1 ]
]
}
}
</source>

The example describes two helices, named A and B, and a β-sheet consisting of three strands, named 1-1, 1-2, and 1-3. Strands 1-1 and 1-2 are connected by an anti-parallel β-ladder, strands 1-2 and 1-3 by a parallel β-ladder. All the SSEs are located on chain A of structure 1tqn.

 
----

[[SecStrAnnotator:UserManual | Back to the main page]]

SecStrAnnotator:UserManual

2021-03-22T21:44:45Z

Midlik:

__NOTOC__

[[File:SecStrAnnotator-annotated-2nnj.png | thumb | right | 400px | Structure of human CYP 2C8 (PDB ID 2nnj) with annotation of the major helices.]]

'''SecStrAnnotator''' is a command line tool for annotation (naming) of '''secondary structure elements (SSEs)''', namely helices and β-strands, in protein structures. It is template-based, meaning that a structurally similar template protein with annotated SSEs is a part of the input.

'''SecStrAnnotator''' alone can be used for '''one-to-one annotation'''. This means that it takes an annotated template protein ''T'' and a query protein ''Q'', it finds SSEs in the query protein ''Q'', and annotates the SSEs in a way that best reflects the annotation of the template ''T''.

'''SecStrAnnotator Suite''' is a set of additional scripts which can be used for '''one-to-many''' annotation. This means that we have a whole protein family, and one of its members serves as the template ''T''. The result is the annotation of all other members of the family. The suite also provides Python and R scripts for a further analysis of the annotation results.

'''SecStrAPI''' provides precomputed SSE annotations (currently only for Cytochrome P450 family).

'''[http://sestra.ncbr.muni.cz SecStrAnnotator Online]''' is a web application allowing you to annotate SSEs without installing the full version of SecStrAnnotator.

'''NEWS:'''

'''SecStrAnnotator 2''' is now available. There are a few basic differences from SecStrAnnotator 1.0:

* SecStrAnnotator 2 is based on .NET Core and it is run using .NET Core Runtime (<code>dotnet</code>). This provides the same behaviour in each operating system.

* The supported structural file format is now mmCIF (PDB file format is not supported anymore). Chain and residue numbering is based on label_* columns in the mmCIF files, not auth_* columns!

 
----
===[[SecStrAnnotator:Introduction | Introduction]]===
----
===[[SecStrAnnotator:OneToOne | Annotation of one query protein (one-to-one)]]===
----
===[[SecStrAnnotator:OneToMany | Annotation of a whole protein family (one-to-many)]]===
----
===[[SecStrAnnotator:Analysis | Analysis of family annotation (case study: Cytochromes P450)]]===
----
===[[SecStrAnnotator:SecStrAPI | SecStrAPI]]===
----
===[[SecStrAnnotator:Download | Download]]===
----
 
If you found '''SecStrAnnotator''' helpful, please cite:

Midlik A, Hutařová Vařeková I, Hutař J, Moturu TR, Navrátilová V, Koča J, Berka K, Svobodová Vařeková R (2019) [https://link.springer.com/protocol/10.1007/978-1-4939-9161-7_3 Automated family-wide annotation of secondary structure elements]. In: Kister AE (ed) Protein supersecondary structures: Methods and protocols, Humana Press. ISBN 978-1-4939-9160-0.
----
{| align=center style="max-width:60em"
|-
| [[File:Elixirlogo.png | 100px]]
| style="width:1em" |
| '''SecStrAnnotator Suite''' is a part of services provided by ELIXIR – European research infrastructure for biological information. For other services provided by ELIXIR's Czech Republic Node visit [https://www.elixir-czech.cz/services www.elixir-czech.cz/services].
|-
|}

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SecStrAnnotator:Analysis

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Midlik:

SecStrAnnotator Suite provides scripts (Python, R) for batch annotation of the whole family and analysis of the annotation results.

==Procedure==

===Data preparation===

The directory <code>scripts/secstrapi_data_preparation/</code> contains a pipeline for annotating the whole protein family, including:

* downloading the list of family members defined by CATH and Pfam,
* downloading their structures,
* selecting a non-redundant set,
* annotation,
* multiple sequence alignment for individual SSEs,
* formatting into [[SecStrAnnotator:SecStrAPI#SecStrAPI_format | SecStrAPI format]],
* formatting into TSV format for further analyses.

The whole pipeline can be executed by <code>scripts/SecStrAPI_pipeline.py</code>

Example usage:

python3 scripts/SecStrAPI_pipeline.py scripts/SecStrAPI_pipeline_settings.json --resume

Before running, modify the settings in <code>SecStrAPI_pipeline_settings.json</code> to set your family of interest, annotation template, data directory etc (see <code>README.txt</code> for more details).

===Data analysis===

The directory <code>scripts/R_sec_str_anatomy_analysis/</code> contains a pipeline for statistical analysis of the annotation results on the whole protein family, including:

* reading the annotation results from TSV,
* generating plots,
* performing statistical test to compare eukaryotic and bacterial structures (or any two sets of structures).

Example usage:

* Launch <code>rstudio</code> from the said directory
* In <code>sec_str_anatomy.R</code>, set DATADIR to the path to your annotation data created in [[#Data preparation]]
* In <code>sec_str_anatomy_settings.R</code>, modify the family-specific settings (list of helices and strands)
* Run <code>sec_str_anatomy.R</code> line by line

==Example case study: Cytochromes P450==

===Data===

For the Cytochrome P450 family, structures of 1855 protein domains are available, located in 1012 PDB entries (updated on 7 July 2020). The analysis was performed on a non-redundant subset containing 183 protein domains.

The data are available [https://doi.org/10.5281/zenodo.3939133 here] (structural files not included because of their size).

===Occurrence of SSEs===

The ''occurrence'' describes in what percentage of the structures a particular SSE is present.

<div><ul>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-occurrence.png | thumb | 500px | Occurrence of particular SSEs in the whole set.]] </li>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-occurrence-Bact-Euka.png | thumb | 500px | Occurrence of particular SSEs – comparison of bacterial and eukaryotic structures.]] </li>
</ul></div>

===Length of SSEs===

The ''length'' of an SSE is measured as the number of residues. The following violin plots show the distribution of length for each SSE.

<div><ul>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-length.png | thumb | 500px | Length distribution of particular SSEs in the whole set. ]] </li>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-length-Bact-Euka.png | thumb | 500px | Length distribution of particular SSEs – comparison of bacterial and eukaryotic structures. ]] </li>
</ul></div>

===Sequence of SSEs===

The amino acid sequences for each SSE can be aligned and used to produce a sequence logo. Where the sequence conservation is sufficient, we can establish a generic numbering scheme: the most conserved residue in helix X serves as its reference residue and is numbered as @X.50. The remaining residues in the helix are numbered accordingly.

<gallery mode="packed" heights=140px caption="Helices">
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File:SecStrAnnotator-cyp-sse-logo-K-.png
File:SecStrAnnotator-cyp-sse-logo-K--.png
File:SecStrAnnotator-cyp-sse-logo-L.png
File:SecStrAnnotator-cyp-sse-logo-L-.png
</gallery>

<gallery mode="packed" heights=140px caption="Beta strands">
File:SecStrAnnotator-cyp-sse-logo-1-0.png
File:SecStrAnnotator-cyp-sse-logo-1-1.png
File:SecStrAnnotator-cyp-sse-logo-1-2.png
File:SecStrAnnotator-cyp-sse-logo-1-3.png
File:SecStrAnnotator-cyp-sse-logo-1-4.png
File:SecStrAnnotator-cyp-sse-logo-1-5.png
File:SecStrAnnotator-cyp-sse-logo-2-1.png
File:SecStrAnnotator-cyp-sse-logo-2-2.png
File:SecStrAnnotator-cyp-sse-logo-3-1.png
File:SecStrAnnotator-cyp-sse-logo-3-2.png
File:SecStrAnnotator-cyp-sse-logo-3-3.png
File:SecStrAnnotator-cyp-sse-logo-4-1.png
File:SecStrAnnotator-cyp-sse-logo-4-2.png
File:SecStrAnnotator-cyp-sse-logo-5-1.png
File:SecStrAnnotator-cyp-sse-logo-5-2.png
File:SecStrAnnotator-cyp-sse-logo-6-1.png
File:SecStrAnnotator-cyp-sse-logo-6-2.png
</gallery>

 
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[[SecStrAnnotator:UserManual | Back to the main page]]

SecStrAnnotator:Download

2020-07-11T09:57:39Z

Midlik:

'''Releases:'''

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.2-release.zip '''SecStrAnnotator 2.2''']

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.1.zip SecStrAnnotator 2.1]

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.0.zip SecStrAnnotator 2.0] (.NET Core application, runs on CIF files)

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_1.0.zip SecStrAnnotator 1.0] (.NET Framework/Mono application, runs on PDB files)

'''Source code:'''

[https://gitlab.com/midlik/SecStrAnnot2 SecStrAnnotator on GitLab]

'''Precomputed annotations:'''

[https://webchem.ncbr.muni.cz/API/SecStr SecStrAPI]

 
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[[SecStrAnnotator:UserManual | Back to the main page]]

SecStrAnnotator:Download

2020-06-19T13:24:15Z

Midlik:

'''Releases:'''

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.1.zip '''SecStrAnnotator 2.1'''] (.NET Core application, runs on CIF files)

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_2.0.zip SecStrAnnotator 2.0] (.NET Core application, runs on CIF files)

[https://is.muni.cz/www/379962/secstrannotator/SecStrAnnotator_1.0.zip SecStrAnnotator 1.0] (.NET Framework/Mono application, runs on PDB files)

'''Source code:'''

[https://gitlab.com/midlik/SecStrAnnot2 SecStrAnnotator on GitLab]

'''Precomputed annotations:'''

[https://webchem.ncbr.muni.cz/API/SecStr SecStrAPI]

 
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[[SecStrAnnotator:UserManual | Back to the main page]]