SecStrAnnotator:OneToMany - Revision history

Midlik: /* Selection of a template domain and obtaining its annotation */

2020-04-09T15:10:22Z

Selection of a template domain and obtaining its annotation

← Older revision		Revision as of 15:10, 9 April 2020
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	In this step, one of the domains from the protein family should be selected as a template domain. Suppose that we have selected the domain which is located on the chain A of PDB entry 2nnj.		In this step, one of the domains from the protein family should be selected as a template domain. Suppose that we have selected the domain which is located on the chain A of PDB entry 2nnj.

	If an SSE annotation of the template domain is available in the literature, it can be converted into the [[SecStrAnnotator:OneToOne#Annotation file format \| ~~required~~ format]] and used as the template annotation.		If an SSE annotation of the template domain is available in the literature, it can be converted into the [[SecStrAnnotator:OneToOne#Annotation file format \| SecStrAnnotator format]] and used as the template annotation.

	If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:		If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:

Midlik at 14:14, 9 April 2020

2020-04-09T14:14:32Z

← Older revision		Revision as of 14:14, 9 April 2020
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	A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).		A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).

	The most of this procedure can be automated by <code>SecStrAPI_master.sh</code> script described in [[SecStrAnnotator:Analysis]]. The part which must be done manually ~~anyway~~ is [[#Selection of a template domain and obtaining its annotation]].		The most of this procedure can be automated by <code>SecStrAPI_master.sh</code> script described in [[SecStrAnnotator:Analysis]]. The part which must be done manually is [[#Selection of a template domain and obtaining its annotation]].

	=Dependencies=		=Dependencies=

Midlik at 14:14, 9 April 2020

2020-04-09T14:14:10Z

← Older revision		Revision as of 14:14, 9 April 2020
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	A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).		A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).

	The ~~described~~ procedure can be automated by <code>SecStrAPI_master.sh</code> script described in [[SecStrAnnotator:Analysis]]. The part which must be done manually anyway is [[#Selection of a template domain and obtaining its annotation]].		The most of this procedure can be automated by <code>SecStrAPI_master.sh</code> script described in [[SecStrAnnotator:Analysis]]. The part which must be done manually anyway is [[#Selection of a template domain and obtaining its annotation]].

	=Dependencies=		=Dependencies=

Midlik at 14:13, 9 April 2020

2020-04-09T14:13:23Z

← Older revision		Revision as of 14:13, 9 April 2020
Line 2:		Line 2:

	A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).		A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).

			The described procedure can be automated by <code>SecStrAPI_master.sh</code> script described in [[SecStrAnnotator:Analysis]]. The part which must be done manually anyway is [[#Selection of a template domain and obtaining its annotation]].

	=Dependencies=		=Dependencies=

Midlik: /* Selection of a template domain and obtaining its annotation */

2020-04-09T14:07:27Z

Selection of a template domain and obtaining its annotation

← Older revision		Revision as of 14:07, 9 April 2020
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	dotnet SecStrAnnotator.dll --onlyssa my_structure_directory 2nnj,A		dotnet SecStrAnnotator.dll --onlyssa my_structure_directory 2nnj,A

	This will create file <code>2nnj-detected.sses.json</code> ~~in <code>my_structure_directory</code>, which should be renamed~~ to <code>2nnj-template.sses.json</code>.		This will create file <code>my_structure_directory/2nnj-detected.sses.json</code>. Rename this file to <code>2nnj-template.sses.json</code> and optionally refine the annotation in the file:

	~~Additional refinement of the template annotation is recommended – this includes removing~~ unnecessary SSEs~~, adding~~ SSEs which should be annotated~~, and possibly renaming~~ the SSEs according to a transparent scheme (e.g. helices A, B, C, D... instead of H0, H1, H4, H6...).		* Remove unnecessary SSEs which you don't want to annotate.
			* Add SSEs which were not detected but should be annotated.
			* Rename the SSEs according to a transparent scheme (e.g. helices A, B, C, D... instead of default H0, H1, H4, H6...).
			* If you add/remove β-strands, don't forget to update also the <code>beta_connectivity</code> section.

	==Running the annotation algorithm on each member of the family==		==Running the annotation algorithm on each member of the family==

Midlik at 13:56, 9 April 2020

2020-04-09T13:56:08Z

← Older revision		Revision as of 13:56, 9 April 2020
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	==Selection of a template domain and obtaining its annotation==		==Selection of a template domain and obtaining its annotation==

	In this step, one of the domains from the protein family should be selected as a template domain. Suppose that we have selected the domain which is located on the chain A of PDB entry ~~1og2~~.		In this step, one of the domains from the protein family should be selected as a template domain. Suppose that we have selected the domain which is located on the chain A of PDB entry 2nnj.

	If an SSE annotation of the template domain is available in the literature, it can be converted into the [[SecStrAnnotator:OneToOne#Annotation file format \| required format]] and used as the template annotation.		If an SSE annotation of the template domain is available in the literature, it can be converted into the [[SecStrAnnotator:OneToOne#Annotation file format \| required format]] and used as the template annotation.
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	If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:		If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:

	dotnet SecStrAnnotator.dll --onlyssa my_structure_directory ~~1og2~~,A		dotnet SecStrAnnotator.dll --onlyssa my_structure_directory 2nnj,A

	This will create file <code>~~1og2~~-detected.sses.json</code> in <code>my_structure_directory</code>, which should be renamed to <code>~~1og2~~-template.sses.json</code>.		This will create file <code>2nnj-detected.sses.json</code> in <code>my_structure_directory</code>, which should be renamed to <code>2nnj-template.sses.json</code>.

	Additional refinement of the template annotation is recommended – this includes removing unnecessary SSEs, adding SSEs which should be annotated, and possibly renaming the SSEs according to a transparent scheme (e.g. helices A, B, C, D... instead of H0, H1, H4, H6...).		Additional refinement of the template annotation is recommended – this includes removing unnecessary SSEs, adding SSEs which should be annotated, and possibly renaming the SSEs according to a transparent scheme (e.g. helices A, B, C, D... instead of H0, H1, H4, H6...).
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	==Running the annotation algorithm on each member of the family==		==Running the annotation algorithm on each member of the family==

	python3 SecStrAnnotator_batch.py my_structure_directory ~~1og2~~,A family_from_cath.json		python3 SecStrAnnotator_batch.py my_structure_directory 2nnj,A family_from_cath.json

	<br style="clear:both" />		<br style="clear:both" />

Midlik: /* Selection of a template domain and obtaining its annotation */

2020-04-09T13:54:38Z

Selection of a template domain and obtaining its annotation

← Older revision		Revision as of 13:54, 9 April 2020
Line 33:		Line 33:
	If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:		If no annotation is available, it must be created from scratch. The easiest way of creating an annotation file is to perform secondary structure assignment (SSA) by SecStrAnnotator:

	~~mono~~ SecStrAnnotator.~~exe~~ --onlyssa my_structure_directory 1og2,A		dotnet SecStrAnnotator.dll --onlyssa my_structure_directory 1og2,A

	This will create file <code>1og2-detected.sses.json</code> in <code>my_structure_directory</code>, which should be renamed to <code>1og2-template.sses.json</code>.		This will create file <code>1og2-detected.sses.json</code> in <code>my_structure_directory</code>, which should be renamed to <code>1og2-template.sses.json</code>.

Midlik: /* Preparing structural data */

2020-04-09T13:53:13Z

Preparing structural data

← Older revision		Revision as of 13:53, 9 April 2020
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	python3 domains_from_pdbeapi.py 1.10.630.10 > family_from_cath.json		python3 domains_from_pdbeapi.py 1.10.630.10 > family_from_cath.json
	or
	python3 domains_from_pdbeapi.py PF00067 > family_from_pfam.json		python3 domains_from_pdbeapi.py PF00067 > family_from_pfam.json

Midlik: /* Selection of a template domain and obtaining its annotation */

2018-05-01T10:36:21Z

Selection of a template domain and obtaining its annotation

← Older revision		Revision as of 10:36, 1 May 2018
Line 37:		Line 37:
	This will create file <code>1og2-detected.sses.json</code> in <code>my_structure_directory</code>, which should be renamed to <code>1og2-template.sses.json</code>.		This will create file <code>1og2-detected.sses.json</code> in <code>my_structure_directory</code>, which should be renamed to <code>1og2-template.sses.json</code>.

	Additional refinement of the template annotation is recommended.		Additional refinement of the template annotation is recommended – this includes removing unnecessary SSEs, adding SSEs which should be annotated, and possibly renaming the SSEs according to a transparent scheme (e.g. helices A, B, C, D... instead of H0, H1, H4, H6...).

	==Running the annotation algorithm on each member of the family==		==Running the annotation algorithm on each member of the family==

Midlik at 10:23, 1 May 2018

2018-05-01T10:23:48Z

← Older revision		Revision as of 10:23, 1 May 2018
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	This page describes the procedure for annotating SSEs in a whole protein family.		This page describes the procedure for annotating SSEs in a whole protein family, using SecStrAnnotator Suite (SecStrAnnotator + supplementary scripts).

	A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).		A '''protein family''' is understood as a set of structurally similar protein domains. A '''protein domain''' can be either a whole protein chain or only a part of it (in multidomain proteins).