ValidatorDB:Terminology - Revision history

Lukas at 15:13, 10 August 2015

2015-08-10T15:13:01Z

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	'''Continue with reading about the [[ValidatorDB:Principles \| ValidatorDB principles]], [[MotiveValidator:~~Functionality~~ \| MotiveValidator functionality]], or return to the [[ValidatorDB:UserManual \| ValidatorDB]], or [[~~MotiveValdiator~~:UserManual \| MotiveValidator]] manuals.'''		'''Continue with reading about the [[ValidatorDB:Principles \| ValidatorDB principles]], [[MotiveValidator:Principles \| MotiveValidator functionality]], or return to the [[ValidatorDB:UserManual \| ValidatorDB]], or [[MotiveValidator:UserManual \| MotiveValidator]] manuals.'''

Lukas at 17:24, 6 August 2015

2015-08-06T17:24:50Z

← Older revision		Revision as of 17:24, 6 August 2015
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	In the validation, ''molecules'' are used as an umbrella term for ''ligands and non-standard residues''. Therefore, all properties of ligands and non-standard residues are valid for molecules as well (PDB entry of origin, residue annotation, residue identifier, number of heavy atoms, properties assigned after the validation, etc.). Moreover, a single occurrence of a ligand or non-standard residue is also a ''molecule''.		In the validation, ''molecules'' are used as an umbrella term for ''ligands and non-standard residues''. Therefore, all properties of ligands and non-standard residues are valid for molecules as well (PDB entry of origin, residue annotation, residue identifier, number of heavy atoms, properties assigned after the validation, etc.). Moreover, a single occurrence of a ligand or non-standard residue is also a ''molecule''.

	It is essential to note that ~~'''~~ValidatorDB~~'''~~ contains validation results for all ligands and non-standard residues containing ''7 or more heavy atoms''. These are denoted as ''molecules relevant for validation'', or simply ''molecules''. The reason ~~'''~~ValidatorDB~~'''~~ focuses on these types of molecules is that they exhibit high diversity and nontriviality in their structure.		It is essential to note that [[ValidatorDB:UserManual \| ValidatorDB]] contains validation results for all ligands and non-standard residues containing ''7 or more heavy atoms''. These are denoted as ''molecules relevant for validation'', or simply ''molecules''. The reason [[ValidatorDB:UserManual \| ValidatorDB]] focuses on these types of molecules is that they exhibit high diversity and nontriviality in their structure.

	=Model=		=Model=
	We use the term ''model'' to refer to a particular structure that is known to be correct. This structure will then be used as reference in the validation process. A model is identified by its residue annotation (3-letter code). The origin of the models used by ~~'''~~ValidatorDB~~'''~~ is the wwPDB Chemical Component Dictionary (wwPDB CCD)<ref name="Sen_2014"/>.		We use the term ''model'' to refer to a particular structure that is known to be correct. This structure will then be used as reference in the validation process. A model is identified by its residue annotation (3-letter code). The origin of the models used both by [[MotiveValidator:UserManual \| MotiveValidator]] and [[ValidatorDB:UserManual \| ValidatorDB]] is the wwPDB Chemical Component Dictionary (wwPDB CCD)<ref name="Sen_2014"/>.

	=Input motif=		=Input motif=
	The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of		The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' is assigned a unique motif identifier during the validation based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.
	one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif~~'' in '''ValidatorDB'~~'' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.

Lukas at 14:48, 18 May 2015

2015-05-18T14:48:00Z

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	The key terms used within the '''ValidatorDB''' environment are defined below. It is important to establish these terms before moving on to the description of the [[ValidatorDB:Principles \| principles]] ~~on which~~ '''~~ValidatorDB~~''' is built.		The key terms used within the '''MotiveValidator''' and '''ValidatorDB''' environment are defined below. It is important to establish these terms before moving on to the description of the [[ValidatorDB:Principles \| '''ValidatorDB''' principles]], or [[MotiveValidator:Functionality \| '''MotiveValidator''' functionality]] on which both validation tools are built.

	=Residue=		=Residue=
	We generally use the term ''residue'' to refer to any component of a biomacromolecule or a biomacromolecular complex. Within the ~~'''ValidatorDB'''~~ environment, a collection of atoms bound by chemical bonds (covalent, coordinative or ionic) can be considered a residue as long as this fact is appropriately indicated in the input PDB file. Specifically, all the atoms that make up a residue should have the same ''residue annotation'' (3-letter code) and ''residue identifier'' (index internal to the PDB file).		We generally use the term ''residue'' to refer to any component of a biomacromolecule or a biomacromolecular complex. Within the validation environment, a collection of atoms bound by chemical bonds (covalent, coordinative or ionic) can be considered a residue as long as this fact is appropriately indicated in the input PDB file. Specifically, all the atoms that make up a residue should have the same ''residue annotation'' (3-letter code) and ''residue identifier'' (index internal to the PDB file).

	=Non-standard residue=		=Non-standard residue=
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	=Ligand=		=Ligand=
	We use the term ''ligand'' to refer to a chemical compound which forms a complex with a biomacromolecule (e.g., sugar, drug, heme). Ions can also function as self standing ligands, or they can be part of a residue (such as Fe in heme). In the PDB format, a ligand has its own residue identifier and annotation (3-letter code), and is composed from HETATM records. The '''~~ValidatorDB~~''' term ''residue'' thus fully covers ligands.		We use the term ''ligand'' to refer to a chemical compound which forms a complex with a biomacromolecule (e.g., sugar, drug, heme). Ions can also function as self standing ligands, or they can be part of a residue (such as Fe in heme). In the PDB format, a ligand has its own residue identifier and annotation (3-letter code), and is composed from HETATM records. The '''validation''' term ''residue'' thus fully covers ligands.

	=Molecule=		=Molecule=
	~~'''ValidatorDB''' uses~~ ''molecules'' as an umbrella term for ''ligands and non-standard residues''. Therefore, all properties of ligands and non-standard residues are valid for molecules as well (PDB entry of origin, residue annotation, residue identifier, number of heavy atoms, properties assigned after the validation, etc.). Moreover, a single occurrence of a ligand or non-standard residue is also a ''molecule''.		In the validation, ''molecules'' are used as an umbrella term for ''ligands and non-standard residues''. Therefore, all properties of ligands and non-standard residues are valid for molecules as well (PDB entry of origin, residue annotation, residue identifier, number of heavy atoms, properties assigned after the validation, etc.). Moreover, a single occurrence of a ligand or non-standard residue is also a ''molecule''.

	It is essential to note that '''ValidatorDB''' contains validation results for all ligands and non-standard residues containing ''7 or more heavy atoms''. These are denoted as ''molecules relevant for validation'', or simply ''molecules''. The reason '''ValidatorDB''' focuses on these types of molecules is that they exhibit high diversity and nontriviality in their structure.		It is essential to note that '''ValidatorDB''' contains validation results for all ligands and non-standard residues containing ''7 or more heavy atoms''. These are denoted as ''molecules relevant for validation'', or simply ''molecules''. The reason '''ValidatorDB''' focuses on these types of molecules is that they exhibit high diversity and nontriviality in their structure.

	=Model=		=Model=
	We use the term ''model'' to refer to a particular structure that is known to be correct. This structure will then be used as reference in the validation process. A model is identified by its residue annotation (3-letter code). The origin of the models used by '''ValidatorDB''' is the wwPDB Chemical Component Dictionary (wwPDB CCD).		We use the term ''model'' to refer to a particular structure that is known to be correct. This structure will then be used as reference in the validation process. A model is identified by its residue annotation (3-letter code). The origin of the models used by '''ValidatorDB''' is the wwPDB Chemical Component Dictionary (wwPDB CCD)<ref name="Sen_2014"/>.

	=Input motif=		=Input motif=
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	'''Continue with reading about the [[ValidatorDB:Principles \| principles]] ~~used in ValidatorDB~~, or return to the [[ValidatorDB:UserManual \| ~~Table of contents~~]].'''		'''Continue with reading about the [[ValidatorDB:Principles \| ValidatorDB principles]], [[MotiveValidator:Functionality \| MotiveValidator functionality]], or return to the [[ValidatorDB:UserManual \| ValidatorDB]], or [[MotiveValdiator:UserManual \| MotiveValidator]] manuals.'''


			=References=
			<references>
			<ref name="Sen_2014">Sen,S., Young,J., Berrisford,J.M., Chen,M., Conroy,M.J., Dutta,S., Di Costanzo,L., Gao,G., Ghosh,S., Hudson,B.P., et al. (2014) [http://dx.doi.org/10.1093/database/bau116 Small molecule annotation for the Protein Data Bank]. Database (Oxford)., 2014, 1–11.</ref>
			</references>

Crina at 22:10, 20 October 2014

2014-10-20T22:10:23Z

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	The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of		The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of
	one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.		one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.


			'''Continue with reading about the [[ValidatorDB:Principles \| principles]] used in ValidatorDB, or return to the [[ValidatorDB:UserManual \| Table of contents]].'''

Crina: /* Motif */

2014-09-08T06:46:30Z

Motif

← Older revision		Revision as of 06:46, 8 September 2014
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	We use the term ''model'' to refer to a particular structure that is known to be correct. This structure will then be used as reference in the validation process. A model is identified by its residue annotation (3-letter code). The origin of the models used by '''ValidatorDB''' is the wwPDB Chemical Component Dictionary (wwPDB CCD).		We use the term ''model'' to refer to a particular structure that is known to be correct. This structure will then be used as reference in the validation process. A model is identified by its residue annotation (3-letter code). The origin of the models used by '''ValidatorDB''' is the wwPDB Chemical Component Dictionary (wwPDB CCD).

	=~~Motif~~=		=Input motif=
	The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of		The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of
	one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.		one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.

Crina at 01:54, 3 September 2014

2014-09-03T01:54:14Z

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	'''ValidatorDB''' ~~is a database of validation results for ligands and non-standard residues in the Protein Data Bank~~. ~~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~~.		The key terms used within the '''ValidatorDB''' environment are defined below. It is important to establish these terms before moving on to the description of the [[ValidatorDB:Principles \| principles]] on which '''ValidatorDB''' is built.

	=Residue=		=Residue=

Crina at 01:40, 3 September 2014

2014-09-03T01:40:31Z

← Older revision		Revision as of 01:40, 3 September 2014
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	The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of		The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of
	one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.		one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.

	[[File:VDB manual figures2.png\|thumb\|right\|700px\|'''A)''' Scheme of the '''validation procedure''' for the entire PDB; '''B)''' Scheme of the '''validation procedure''' for a sialic acid (''SIA'') molecule in PDB entry ''4jtv''; '''C)''' Typical '''validation results''' for ''SIA'' molecules.]]

	~~=Validation procedure=~~
	Within the '''ValidatorDB''' environment, the term ''validation'' refers to the process of determining whether a molecule is structurally complete and correctly annotated. This means checking if the topology and chirality of each validated molecule correspond to those of the model with the same annotation (3-letter code) as the validated molecule.

	'''ValidatorDB''' implements the ''validation of annotation'' approach, which consists of several steps. First, for each molecule under investigation, the ''input motif'' is extracted from the respective PDB entry. At the same time, the appropriate ''model'' is retrieved from wwPDB CCD. Then, the ''validated molecule'' (or ''validated motif'') is identified as the subset of atoms common in the ''model'' and the ''input motif''. Subsequently, the ''validated molecule'' is compared against the ''model'', atom by atom. All the validation analyses in '''ValidatorDB''' are based on this comparison of atom properties (presence, chirality, element symbol, PDB name, etc.). Other unusual aspects encountered during validation are reported as processing warnings (e.g., which conformer was validated if several conformers were present).

	~~=Validation analyses=~~
	The validation analyses performed by ValidatorDB cover all main issues which have been observed in the topology (2D structure) and geometry (3D structure) of ligands and non-standard residues. These validation analyses, along with their respective results, can be classified into three categories, namely ''Completeness'', ''Chirality'' and ''Advanced'' analyses.

	The ''Completeness'' analyses attempt to find which atoms are missing, whether these atoms are part of rings, or the structure is degenerate, i.e., the molecule contains very severe errors. These may refer to residues overlapping in the 3D space, or atoms which are disconnected from the rest of the structure.

	The ''Chirality'' analyses are performed only on complete structures, and aim to evaluate the chirality of each atom in the validated molecule. We distinguish between several types of chirality errors: on carbon atoms (C chirality), on metal atoms (Metal chirality), on atoms with 4 substituents in one plane (Planar chirality), on atoms connected to at least one substituent by a bond of higher order (High order chirality), and the remaining chirality issues (Other chirality).

	The ''Advanced'' analyses are focused on issues which are not real chemical problems, but which can complicate further processing and exploration of data, and thus should be noted. The Substitution analysis reports the replacement of some atom by an atom of a different chemical element. The Foreign atom analysis detects atoms which originate from the neighborhood of the validated molecule (i.e., having different PDB residue ID than the majority of the validated molecule), and generally marks sites of inter-molecular linkage. The Different naming analysis identifies atoms whose name in PDB format is different than the standard convention for the validated molecule. The Zero RMSD analysis reports molecules whose structure is identical (root mean square deviation = 0 Å) to the model from wwPDB CCD. The Alternate conformations analysis informs about the occurrence of alternate conformations in the validated PDB entry.

	~~=Validation results=~~
	Each molecule is evaluated depending on how it fares during the validation analyses described above. If no issues are found during the validation analyses, the molecule is marked as having ''complete structure and correct chirality''. Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''. If no issues are detected during the ''Chirality'' analyses, the validated molecule is marked as having ''Correct chirality'', whereas the remaining molecules are marked as having ''Wrong chirality''. When issues are found during an ''Advanced'' analysis, a warning is reported: Substitution, Foreign atom, Different naming, Zero RMSD or Alternate conformations. Each type of issue encountered during validation has a specific color code.

	Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model from wwPDB CCD. Further, an error in high order chirality often marks the involvement of phosphate O atoms in salt or ester formation, or merely a different PDB format identification of phosphate O atoms of the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having ''Correct chirality (tolerant)''.

	While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.

	~~=Validation reports=~~
	For each PDB entry, the relevant molecules are detected and validated. '''ValidatorDB''' is then built as the collection of validation results for all molecules in all PDB entries. The results are systematically organized into reports:
	* Validation overview for the entire PDB
	* Summary of validation results for sets of molecules sharing the same annotation
	* Summary of validation results for sets of molecules originating from the same PDB entry
	* Detailed validation report for a set of molecules sharing a particular annotation
	* Detailed validation report for a particular PDB entry
	* Detailed validation report for a particular molecule
	* Custom validation report

	~~Each type of validation report is accessible via different sections of the web interface (.................)~~

Crina at 01:13, 3 September 2014

2014-09-03T01:13:53Z

← Older revision		Revision as of 01:13, 3 September 2014
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	=Molecule=		=Molecule=
	'''ValidatorDB''' uses ''molecules'' as an umbrella term for ''ligands and non-standard residues''. Therefore, all properties of ligands and non-standard residues are valid for molecules as well (PDB entry of origin, residue annotation, residue identifier, number of heavy atoms, properties assigned after the validation, etc.). Moreover, a single occurrence of a ligand or non-standard residue is also a ''molecule''. ~~Furthermore, it~~ is essential to note that '''ValidatorDB''' contains validation results for all ligands and non-standard residues containing ''7 or more heavy atoms''. These are denoted as ''molecules relevant for validation'', or simply ''molecules''.		'''ValidatorDB''' uses ''molecules'' as an umbrella term for ''ligands and non-standard residues''. Therefore, all properties of ligands and non-standard residues are valid for molecules as well (PDB entry of origin, residue annotation, residue identifier, number of heavy atoms, properties assigned after the validation, etc.). Moreover, a single occurrence of a ligand or non-standard residue is also a ''molecule''.

			It is essential to note that '''ValidatorDB''' contains validation results for all ligands and non-standard residues containing ''7 or more heavy atoms''. These are denoted as ''molecules relevant for validation'', or simply ''molecules''. The reason '''ValidatorDB''' focuses on these types of molecules is that they exhibit high diversity and nontriviality in their structure.

	=Model=		=Model=
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	The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of		The term ''motif'' is used here as a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of
	one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.		one or more residues or parts of residues. Specifically, the term ''input motif'' refers to the individual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Each ''input motif'' in '''ValidatorDB''' is assigned a unique motif identifier based on its PDB entry of origin. On the other hand, the term ''validated motif'' (or ''validated molecule'') refers strictly to the subset of atoms in the ''input motif'' which were successfully mapped to atoms in the ''model''.

			[[File:VDB manual figures2.png\|thumb\|right\|700px\|'''A)''' Scheme of the '''validation procedure''' for the entire PDB; '''B)''' Scheme of the '''validation procedure''' for a sialic acid (''SIA'') molecule in PDB entry ''4jtv''; '''C)''' Typical '''validation results''' for ''SIA'' molecules.]]

	=Validation procedure=		=Validation procedure=
	'''ValidatorDB''' implements the ''validation of annotation'' approach, which consists of several steps. First, for each molecule under investigation, the ''input motif'' is extracted from the respective PDB entry. At the same time, the appropriate ''model'' is retrieved from wwPDB CCD. Then, the ''validated molecule'' (or ''validated motif'') is identified as the subset of atoms common in the ''model'' and the ''input motif''. Subsequently, the ''validated molecule'' is compared against the ''model'', atom by atom. All the validation analyses in '''ValidatorDB''' are based on this comparison of atom properties (presence, chirality, element symbol, PDB name, etc.). Other unusual aspects encountered during validation are reported as processing warnings (e.g., which conformer was validated if several conformers were present)~~. Refer to figure.................~~.		Within the '''ValidatorDB''' environment, the term ''validation'' refers to the process of determining whether a molecule is structurally complete and correctly annotated. This means checking if the topology and chirality of each validated molecule correspond to those of the model with the same annotation (3-letter code) as the validated molecule.

			'''ValidatorDB''' implements the ''validation of annotation'' approach, which consists of several steps. First, for each molecule under investigation, the ''input motif'' is extracted from the respective PDB entry. At the same time, the appropriate ''model'' is retrieved from wwPDB CCD. Then, the ''validated molecule'' (or ''validated motif'') is identified as the subset of atoms common in the ''model'' and the ''input motif''. Subsequently, the ''validated molecule'' is compared against the ''model'', atom by atom. All the validation analyses in '''ValidatorDB''' are based on this comparison of atom properties (presence, chirality, element symbol, PDB name, etc.). Other unusual aspects encountered during validation are reported as processing warnings (e.g., which conformer was validated if several conformers were present).

	=Validation analyses=		=Validation analyses=
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	=Validation results=		=Validation results=
	Each molecule is evaluated depending on how it fares during the validation analyses described above. If no issues are found during the validation analyses, the molecule is marked as having ''complete structure and correct chirality''. Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''. If no issues are detected during the ''Chirality'' analyses, the validated molecule is marked as having ''Correct chirality'', whereas the remaining molecules are marked as having ''Wrong chirality''.		Each molecule is evaluated depending on how it fares during the validation analyses described above. If no issues are found during the validation analyses, the molecule is marked as having ''complete structure and correct chirality''. Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''. If no issues are detected during the ''Chirality'' analyses, the validated molecule is marked as having ''Correct chirality'', whereas the remaining molecules are marked as having ''Wrong chirality''. When issues are found during an ''Advanced'' analysis, a warning is reported: Substitution, Foreign atom, Different naming, Zero RMSD or Alternate conformations. Each type of issue encountered during validation has a specific color code.

	Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model from wwPDB CCD. Further, an error in high order chirality often marks the involvement of phosphate O atoms in salt or ester formation, or merely a different PDB format identification of phosphate O atoms of the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having ''Correct chirality (tolerant)''.		Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model from wwPDB CCD. Further, an error in high order chirality often marks the involvement of phosphate O atoms in salt or ester formation, or merely a different PDB format identification of phosphate O atoms of the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having ''Correct chirality (tolerant)''.

	~~When issues are found during an ''Advanced'' analysis, a warning is reported: Substitution, Foreign atom, Different naming, Zero RMSD or Alternate conformations.~~ While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.		While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.

	=Validation reports=		=Validation reports=
	In '''ValidatorDB''', the ~~results~~ of ~~the~~ validation ~~analyses~~ are organized ~~systematically~~:		For each PDB entry, the relevant molecules are detected and validated. '''ValidatorDB''' is then built as the collection of validation results for all molecules in all PDB entries. The results are systematically organized into reports:
	* Validation overview for the entire PDB~~: summarizes the results of all validation analyses for all molecules~~		* Validation overview for the entire PDB
	* Summary of validation results for sets of molecules sharing the same annotation		* Summary of validation results for sets of molecules sharing the same annotation
	* Summary of validation results for sets of molecules originating from the same PDB entry		* Summary of validation results for sets of molecules originating from the same PDB entry

Crina at 00:43, 3 September 2014

2014-09-03T00:43:34Z

Show changes

Crina: Created page with "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] envir..."

2014-09-02T15:23:13Z

Created page with "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] envir..."

New page

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.

=Ligand=
We use the term ''ligand'' to refer to a chemical compound which forms a complex with a biomacromolecule (e.g., sugar, drug, heme). Ions can also function as self standing ligands, or they can be part of a residue (such as Fe in heme). In the PDB format, a ligand has its own residue identifier and 3-letter code, and is composed from HETATM records. The '''ValidatorDB''' term [[#Residue | residue]] thus fully covers ligands, in addition to typical components like amino acids and nucleotides.

=Residue=
We generally use the term ''residue'' to refer to any component of a biomacromolecule or a biomacromolecular complex. This includes amino acid residues and nucleotides, which are commonly referred to as residues as they form proteins and nucleic acids. Within the '''MotiveValidator''' environment, any collection of atoms bound by chemical bonds (covalent, coordinative or ionic) can be considered a residue as long as this fact is appropriately indicated in the input PDB file. Specifically, all the atoms that make up a residue should have the same ''residue annotation'' (3-letter code) and ''residue identifier'' (index internal to the input PDB file).

=Non-standard residue=
'''ValidatorDB''' does not cover the 5 standard nucleotides and their common deoxy- forms, the 20 standard amino acids and selenomethionine (MSE). Validation results for the standard building blocks of biomacromolecules are not included in our database because many tools already cover these. Additionally, MSE is also excluded from validation due to its extremely high occurrence in the PDB (markedly higher than other ligands and non-standard residues), and high incidence of circumstantial inclusion in biomacromolecules (to aid X-ray crystallography experiments). Therefore, '''ValidatorDB''' covers only ''non-standard residues''.

=Molecules relevant for validation=
'''ValidatorDB''' covers all ligands and non-standard residues containing 7 or more heavy atoms.

Within the '''MotiveValidator''' environment, a ''motif'' is generally a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of
one or more residues or parts of residues. A ''motif'' can in principle be any fragment of a biomolecule. Nonetheless, '''MotiveValidator''' is focused on the validation of residues, thus here ''motif'' generally
refers to a fragment made up from the residue under study, together with its surroundings (i.e., atoms from neighboring residues). Note that the terms ''fragment'' and ''motif'' are used as synonyms in this manual.

=Motif=
Only input motif or validated motif (=validated molecule)
With respect to the chemistry of biomolecules, the term ''motif'' is used to refer to a well defined distribution of structural elements in a biomolecule or biomolecular complex, with characteristics
generally associated with a specific function. Within the '''MotiveValidator''' environment, a ''motif'' is generally a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of
one or more residues or parts of residues. A ''motif'' can in principle be any fragment of a biomolecule. Nonetheless, '''MotiveValidator''' is focused on the validation of residues, thus here ''motif'' generally
refers to a fragment made up from the residue under study, together with its surroundings (i.e., atoms from neighboring residues). Note that the terms ''fragment'' and ''motif'' are used as synonyms in this manual.

We can generally say that, within the '''MotiveValidator''' environment, all ''residues'' can be thought of as ''motifs''. Therefore, different ''instances of the same residue'' (such as multiple arginine residues throughout the sequence of a protein, or copies of the same ligand in different monomers) can be considered and processed as different ''motifs'', making their identification straightforward and unambiguous.

We use the term model residue (or simply model) to refer to a particular structure that is known to be correct. This structure will then be used as reference template in the validation process, whereby a query residue with the same name (3-letter code) as the model will be compared to the model. Within the '''MotiveValidator''' environment, a model contains one residue. The origin of the model can be the wwPDB chemical component dictionary accessible via LigandExpo, or a custom model provided by the user.

=Validation terminology=
* '''Model residue:''' Or simply ''model'' is a particular structure that is known to be correct. This structure is then used as reference template in the validation process, whereby a query residue with the same name (3-letter code) as the model will be compared to the model. Within the ''MotiveValidator'' environment, a model contains one residue. The origin of the ''model'' can be the wwPDB chemical component dictionary accessible via LigandExpo<ref name ="ligandexpo"/>, or a custom model provided by the user.
* '''Residue to be validated (validated residue):''' Residue of interest for validation.
* '''Input motif:''' Residues to be validated together with their immediate surroundings (i.e. atoms within one or two bonds of any atom of the residue to be validated).
* '''Validated motif:''' The subset of atoms from the input motif paired with atoms in the model residue.

=References=
<references>
<ref name="ligandexpo">Feng,Z., Chen,L., Maddula,H., Akcan,O., Oughtred,R., Berman,H.M. and Westbrook,J. (2004) [http://dx.doi.org/10.1093/bioinformatics/bth214 Ligand Depot: a data warehouse for ligands bound to macromolecules]. Bioinformatics, 20, 2153–5.</ref>
</references>