ValidatorDB - Revision history

Lukas: Replaced content with "Content of this page was moved here."

2014-10-07T10:44:19Z

Replaced content with "Content of this page was moved here."

Lukas at 09:58, 14 August 2014

2014-08-14T09:58:53Z

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	The advancement of research in structural biology has provided a large body of structural data deposited in various databases. One great example is the Protein Data Bank (PDB), which has been growing exponentially, and which currently consists of more than 100,000 structures of biomolecules and their complexes. Such large bodies of data, especially accumulated over a short period of time using high throughput techniques, will inherently be plagued by various problems.		The advancement of research in structural biology has provided a large body of structural data deposited in various databases. One great example is the Protein Data Bank (PDB), which has been growing exponentially, and which currently consists of more than 100,000 structures of biomolecules and their complexes. Such large bodies of data, especially accumulated over a short period of time using high throughput techniques, will inherently be plagued by various problems.

	Validation arose as a major issue in the structural biology community when it became apparent that some published structures contained serious errors, and only sometimes it is properly explained (e.g., due to insufficient electron density in a certain area). Structural databases generally require that the new submissions be checked prior to acceptance. The tools employed for presubmission validations work fairly well for residues like amino acids or nucleotides. However, an essential step in the validation process is checking the ligand structure, because ligands play a key role in protein function, and also because they are the main source of errors in structures. Ligand validation, as well as the validation of uncommon residues, are very challenging tasks, because of the high diversity and nontriviality of their structure, and the general lack of information about correct structures. Therefore, software tools focused on ligand validation were developed relatively recently, <ref name="Lutteke_2004"/><ref name="Kleywegt_2007"/> and the topic is still under active development<ref name="~~ftp~~"/>. These tools are able to validate one or more structures (even thousands of structures), but they are not able to provide the broad scientific community with a more complex image of the quality of structures in dedicated and well established structural databases. For example, a general overview and corresponding statistical evaluation of validation results for residues and ligands in the entire PDB is not yet available, despite the exponential growth of the PDB and the development of structural validation tools in recent years.		Validation arose as a major issue in the structural biology community when it became apparent that some published structures contained serious errors, and only sometimes it is properly explained (e.g., due to insufficient electron density in a certain area). Structural databases generally require that the new submissions be checked prior to acceptance. The tools employed for presubmission validations work fairly well for residues like amino acids or nucleotides. However, an essential step in the validation process is checking the ligand structure, because ligands play a key role in protein function, and also because they are the main source of errors in structures. Ligand validation, as well as the validation of uncommon residues, are very challenging tasks, because of the high diversity and nontriviality of their structure, and the general lack of information about correct structures. Therefore, software tools focused on ligand validation were developed relatively recently, <ref name="Lutteke_2004"/><ref name="Kleywegt_2007"/> and the topic is still under active development<ref name="Berman_2014"/>. These tools are able to validate one or more structures (even thousands of structures), but they are not able to provide the broad scientific community with a more complex image of the quality of structures in dedicated and well established structural databases. For example, a general overview and corresponding statistical evaluation of validation results for residues and ligands in the entire PDB is not yet available, despite the exponential growth of the PDB and the development of structural validation tools in recent years.

	We had recently developed MotiveValidator<ref name="Varekova_2014"/>, an interactive platform for the speedy validation of ligands, residues and fragments using a novel, straightforward approach based on the validation of residue annotation. MotiveValidator employs advanced algorithms for the detection and comparison of structural motifs<ref name="Sehnal_2012"/>, along with tools for chirality verification<ref name="Boyle_2011" /> and interactive visualization of 3D structures<ref name="web"/>. Using MotiveValidator, we further created '''ValidatorDB''', a comprehensive resource of validation results for residues and ligands in the [http://pdb.org/pdb/home/home.do \| Protein Data Bank]. Along with validation results for individual residues and ligands, '''ValidatorDB''' also provides a summary and statistical evaluation of the validation results at various levels of detail within the PDB. Thus, '''ValidatorDB''' offers a comprehensive overview of the quality of the ligand structures in the entire PDB. '''ValidatorDB''' contains precomputed validation results for ligands and residues in the Protein Data Bank. The database is updated on a weekly basis.		We had recently developed MotiveValidator<ref name="Varekova_2014"/>, an interactive platform for the speedy validation of ligands, residues and fragments using a novel, straightforward approach based on the validation of residue annotation. MotiveValidator employs advanced algorithms for the detection and comparison of structural motifs<ref name="Sehnal_2012"/>, along with tools for chirality verification<ref name="Boyle_2011" /> and interactive visualization of 3D structures<ref name="web"/>. Using MotiveValidator, we further created '''ValidatorDB''', a comprehensive resource of validation results for residues and ligands in the [http://pdb.org/pdb/home/home.do \| Protein Data Bank]. Along with validation results for individual residues and ligands, '''ValidatorDB''' also provides a summary and statistical evaluation of the validation results at various levels of detail within the PDB. Thus, '''ValidatorDB''' offers a comprehensive overview of the quality of the ligand structures in the entire PDB. '''ValidatorDB''' contains precomputed validation results for ligands and residues in the Protein Data Bank. The database is updated on a weekly basis.
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	<ref name="Kleywegt_2007">Kleywegt,G.J. and Harris,M.R. (2007) [http://dx.doi.org/10.1107/S090744490703315X ValLigURL: a server for ligand-structure comparison and validation.] Acta Crystallogr. D. Biol. Crystallogr., 63, 935–8.</ref>		<ref name="Kleywegt_2007">Kleywegt,G.J. and Harris,M.R. (2007) [http://dx.doi.org/10.1107/S090744490703315X ValLigURL: a server for ligand-structure comparison and validation.] Acta Crystallogr. D. Biol. Crystallogr., 63, 935–8.</ref>

	<ref name="~~ftp~~">~~ftp~~://~~ftp~~.~~ebi~~.ac.~~uk/pub/databases/pdb/validation_reports~~/</ref>		<ref name="Berman_2014">Berman, H.M., Kleywegt, G.J., Nakamura, H. and Markley, J.L. (2014) [http://dx.doi.org/10.1007/s10822-014-9770-y The Protein Data Bank archive as an open data resource]. J. Comput. Aided. Mol. Des. </ref>

	<ref name="Varekova_2014">Vařeková,R.S., Jaiswal,D., Sehnal,D., Ionescu,C.-M., Geidl,S., Pravda,L., Horský,V., Wimmerová,M. and Koča,J. (2014) [http://dx.doi.org/10.1093/nar/gku426 MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes]. Nucleic Acids Res., 12, 227–233.</ref>		<ref name="Varekova_2014">Vařeková,R.S., Jaiswal,D., Sehnal,D., Ionescu,C.-M., Geidl,S., Pravda,L., Horský,V., Wimmerová,M. and Koča,J. (2014) [http://dx.doi.org/10.1093/nar/gku426 MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes]. Nucleic Acids Res., 12, 227–233.</ref>

Lukas: /* Validation */

2014-08-14T09:55:19Z

Validation

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	<b>B)</b> Example of validation for a ~~galactose~~ (''~~GAL~~'') motif in the PDB entry ''~~1bzw~~''. The validated residue ''~~GAL~~'' is extracted from PDB entry ''~~1bzw~~'' in the form of an input motif, which contains all the atoms of the validated residue, together with all atoms found within one or two bonds of any atom from the validated residue (surroundings). By superimposing the input motif and model residue, the validated motif results as the subset of atoms in the input motif which correspond to atoms in the model residue. Evaluation of the validated motif (which atoms are present and where, compared to the model residue) produces the validation results.		<b>B)</b> Example of validation for a sialic acid (''SIA'') motif in the PDB entry ''4jtv''. The validated residue ''SIA'' is extracted from PDB entry ''4jtv'' in the form of an input motif, which contains all the atoms of the validated residue, together with all atoms found within one or two bonds of any atom from the validated residue (surroundings). By superimposing the input motif and model residue, the validated motif results as the subset of atoms in the input motif which correspond to atoms in the model residue. Evaluation of the validated motif (which atoms are present and where, compared to the model residue) produces the validation results.




	<b>C)</b> Typical validation results for a ''~~GAL~~'' motif. If the validated motif contains all atoms at their expected positions, it is marked as correct (green). If any atoms are missing, the validated motif is marked as <span style="color:#FF0000">incomplete (red)</span>. If some atoms have <span style="color:#DAA520">wrong chirality</span>, the validated motif is marked accordingly <span style="color:#DAA520">(dark yellow)</span>. If any unusual features are detected, the validated motif is marked with a <span style="color:#008B8B">warning (cyan)</span> (not shown). The full list of graphical results is available [[ValidatorDB:Analysis_of_Results \| here]].		<b>C)</b> Typical validation results for a ''SIA'' motif. If the validated motif contains all atoms at their expected positions, it is marked as correct (green). If any atoms are missing, the validated motif is marked as <span style="color:#FF0000">incomplete (red)</span>. If some atoms have <span style="color:#DAA520">wrong chirality</span>, the validated motif is marked accordingly <span style="color:#DAA520">(dark yellow)</span>. If any unusual features are detected, the validated motif is marked with a <span style="color:#008B8B">warning (cyan)</span> (not shown). The full list of graphical results is available [[ValidatorDB:Analysis_of_Results \| here]].

Lukas at 11:19, 12 August 2014

2014-08-12T11:19:30Z

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	<span style="font-size:150%; line-height: 1.3em;">If you are a first time user, please visit our introduction to '''[~~[ValidatorDB~~:~~UI \|~~ ValidatorDB]]''', [[MotiveValidator:Terminology \| Terminology]] used within following lines or [[ValidatorDB:Analysis_of_Results \| results analysis]].</span>		<span style="font-size:150%; line-height: 1.3em;">If you are a first time user, please visit our introduction to '''[http://www.slideshare.net/lukypravda/validatordb-first-time-user-guide-37728902 ValidatorDB]''', [[MotiveValidator:Terminology \| Terminology]] used within following lines or [[ValidatorDB:Analysis_of_Results \| results analysis]].</span>

Lukas: /* Validation */

2014-08-05T15:23:35Z

Validation

← Older revision		Revision as of 15:23, 5 August 2014
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	The validation of residues and ligands in the entire PDB takes place in a few distinct steps. First, for each PDB entry, the residues which are relevant for validation are detected based on their name (3-letter code) and number of atoms (more than 6 heavy atoms). Amino acid residues and nucleotides are excluded based on their residue name. Then, for each validated residue, the corresponding model (same 3-letter code as the validated residue) is retrieved from wwPDB CCD, and each motif of this residue is validated against the model.		The validation of residues and ligands in the entire PDB takes place in a few distinct steps. First, for each PDB entry, the residues which are relevant for validation are detected based on their name (3-letter code) and number of atoms (more than 6 heavy atoms). Amino acid residues and nucleotides are excluded based on their residue name. Then, for each validated residue, the corresponding model (same 3-letter code as the validated residue) is retrieved from wwPDB CCD, and each motif of this residue is validated against the model.

			<br style="clear:both" />

	===Validation results===		===Validation results===

Lukas: /* Validation */

2014-08-05T15:22:23Z

Validation

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	===Validation===		===Validation===
	~~TODO - infographics~~		[[File:VDB manual figures2.png\|thumb\|right\|700px\|'''Validation process''']]
	[[File:VDB manual figures2.png\|thumb\|~~centre~~\|~~500px~~\|'''Validation process''']]


	<b>A)</b> Overview of validation process. For each PDB entry, the relevant [[MotiveValidator:Terminology#Residue \| residues]] are detected based on their name (3-letter code) and number of atoms. Then, for each [[MotiveValidator:Terminology#Validation_terminology \| validated residue]], the corresponding model is retrieved from wwPDB CCD, and each motif of this residue is validated against the model. '''ValidatorDB''' is then built as the collection of validation results for all motifs of all residues in all PDB entries.		<b>A)</b> Overview of validation process. For each PDB entry, the relevant [[MotiveValidator:Terminology#Residue \| residues]] are detected based on their name (3-letter code) and number of atoms. Then, for each [[MotiveValidator:Terminology#Validation_terminology \| validated residue]], the corresponding model is retrieved from wwPDB CCD, and each motif of this residue is validated against the model. '''ValidatorDB''' is then built as the collection of validation results for all motifs of all residues in all PDB entries.




	<b>B)</b> Example of validation for a galactose (''GAL'') motif in the PDB entry ''1bzw''. The validated residue ''GAL'' is extracted from PDB entry ''1bzw'' in the form of an input motif, which contains all the atoms of the validated residue, together with all atoms found within one or two bonds of any atom from the validated residue (surroundings). By superimposing the input motif and model residue, the validated motif results as the subset of atoms in the input motif which correspond to atoms in the model residue. Evaluation of the validated motif (which atoms are present and where, compared to the model residue) produces the validation results.		<b>B)</b> Example of validation for a galactose (''GAL'') motif in the PDB entry ''1bzw''. The validated residue ''GAL'' is extracted from PDB entry ''1bzw'' in the form of an input motif, which contains all the atoms of the validated residue, together with all atoms found within one or two bonds of any atom from the validated residue (surroundings). By superimposing the input motif and model residue, the validated motif results as the subset of atoms in the input motif which correspond to atoms in the model residue. Evaluation of the validated motif (which atoms are present and where, compared to the model residue) produces the validation results.

	<b>C)</b> Typical validation results for a ''GAL'' motif. If the validated motif contains all atoms at their expected positions, it is marked as correct (green). If any atoms are missing, the validated motif is marked as <span style="color:#FF0000">incomplete (red)</span>. If some atoms have <span style="color:#DAA520">wrong chirality</span>, the validated motif is marked accordingly <span style="color:#DAA520">(dark yellow)</span>. If any unusual features are detected, the validated motif is marked with a <span style="color:#008B8B">warning (cyan)</span>.


			<b>C)</b> Typical validation results for a ''GAL'' motif. If the validated motif contains all atoms at their expected positions, it is marked as correct (green). If any atoms are missing, the validated motif is marked as <span style="color:#FF0000">incomplete (red)</span>. If some atoms have <span style="color:#DAA520">wrong chirality</span>, the validated motif is marked accordingly <span style="color:#DAA520">(dark yellow)</span>. If any unusual features are detected, the validated motif is marked with a <span style="color:#008B8B">warning (cyan)</span> (not shown). The full list of graphical results is available [[ValidatorDB:Analysis_of_Results \| here]].




	Within the '''ValidatorDB''' environment, the term validation refers to the process of determining whether a residue or ligand is structurally complete and correctly annotated. This means checking if the topology and chirality of each [[MotiveValidator:Terminology#Motif_/_Fragment \|motif]] of a [[MotiveValidator:Terminology#Validation_terminology\| validated residue]] correspond to those of the [[MotiveValidator:Terminology#Validation_terminology\|model residue]] with the same name as the validated residue.		Within the '''ValidatorDB''' environment, the term validation refers to the process of determining whether a residue or ligand is structurally complete and correctly annotated. This means checking if the topology and chirality of each [[MotiveValidator:Terminology#Motif_/_Fragment \|motif]] of a [[MotiveValidator:Terminology#Validation_terminology\| validated residue]] correspond to those of the [[MotiveValidator:Terminology#Validation_terminology\|model residue]] with the same name as the validated residue.


	The validation of residues and ligands in the entire PDB takes place in a few distinct steps. First, for each PDB entry, the residues which are relevant for validation are detected based on their name (3-letter code) and number of atoms (more than 6 heavy atoms). Amino acid residues and nucleotides are excluded based on their residue name. Then, for each validated residue, the corresponding model (same 3-letter code as the validated residue) is retrieved from wwPDB CCD, and each motif of this residue is validated against the model.		The validation of residues and ligands in the entire PDB takes place in a few distinct steps. First, for each PDB entry, the residues which are relevant for validation are detected based on their name (3-letter code) and number of atoms (more than 6 heavy atoms). Amino acid residues and nucleotides are excluded based on their residue name. Then, for each validated residue, the corresponding model (same 3-letter code as the validated residue) is retrieved from wwPDB CCD, and each motif of this residue is validated against the model.

Lukas at 22:14, 30 July 2014

2014-07-30T22:14:53Z

Show changes

Lukas: /* Custom Search */

2014-07-29T11:12:31Z

Custom Search

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	====Custom Search====		====Custom Search====

	The '''Custom Search''' tab allows you to create your own view of the ligands validation of the PDB database. Simply paste a list of you you desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text box separated by commas or a newline. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the ~~glycosyltransferase~~. Note that you can retrieve such lists by using [http://www.rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.		The '''Custom Search''' tab allows you to create your own view of the ligands validation of the PDB database. Simply paste a list of you you desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text box separated by commas or a newline. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the ''glycosyltransferases'' or ''nmr structures''. Note that you can retrieve such lists by using [http://www.rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.

Lukas: /* Custom Search */

2014-07-29T11:12:00Z

Custom Search

← Older revision		Revision as of 11:12, 29 July 2014
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	====Custom Search====		====Custom Search====

	The '''Custom Search''' tab allows you to create your own view of the ligands validation of the PDB database. Simply paste a list of you you desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text box separated by commas or a newline. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the glycosyltransferase. Note that you can retrieve such lists by using [[http://www.rcsb.org/pdb/search/advSearch.do \| advanced search in PDB]]. Also bear in mind, that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.		The '''Custom Search''' tab allows you to create your own view of the ligands validation of the PDB database. Simply paste a list of you you desired ligands (3-letter code) and/or PDB entries (4-letter code) in provided text box separated by commas or a newline. This is particularly convenient in case you need to retrieve a validation report for a huge number of structures. Such as all the glycosyltransferase. Note that you can retrieve such lists by using [http://www.rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.

Lukas: /* How to get around the web page */

2014-07-29T11:10:33Z

How to get around the web page

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	===How to get around the web page===		===How to get around the web page===

	For the quick tour on using ValidatorDB service, please go '''[[ValidatorDB:UI\|HERE]]'''. Whenever you are unsure about the function of different user interface elements, please click the '?' button for the guide.		For the quick tour on using '''ValidatorDB''' service, please go '''[[ValidatorDB:UI\|HERE]]'''. Whenever you are unsure about the function of different user interface elements, please click the '?' button for the guide.

	Before moving on to more extensive descriptions of features, it is important to clearly establish the meaning of a few key terms and principles within the ValidatorDB environment. See [[MotiveValidator:Terminology\|Terminology]].		Before moving on to more extensive descriptions of features, it is important to clearly establish the meaning of a few key terms and principles within the ValidatorDB environment. See [[MotiveValidator:Terminology\|Terminology]].