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ValidatorDB:Terminology

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Before moving on to more extensive descriptions of features, it The key terms used within the '''MotiveValidator''' and '''ValidatorDB''' environment are defined below. It is important to clearly establish these terms before moving on to the meaning description of a few key terms and principles within the [[ValidatorDB] environment. =Ligand=We use the term :Principles | '''ValidatorDB'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 ligandsprinciples]], 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 [[MotiveValidator:Functionality | '''ValidatorDBMotiveValidator''' term [[#Residue | residuefunctionality]] thus fully covers ligands, in addition to typical components like amino acids and nucleotideson which both validation tools are built.
=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''' validation environment, any 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 input PDB file).
=Non-standard residue=
With respect to the building blocks of biomacromolecules, '''ValidatorDB''' does not cover denotes as ''standard residues'' the 5 standard nucleotides and (A, C, G, T, U) together with their 5 common deoxy- forms(DA, DC, DG, DT, DU), and the 20 standard amino acids and selenomethionine (MSE). Validation results for the these standard building blocks of biomacromolecules are not included in our database because many tools already cover these. Additionally, Selenomethionine (MSE ) is also excluded from validation considered a ''standard residue'' here due to its extremely high occurrence in the PDB Protein Data Bank (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'', i.e., residues which cannot be denoted as ''standard'' by the above definition. =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 '''validation''' term ''residue'' thus fully covers ligands.
=Molecules relevant for validationMolecule=In the validation, ''molecules''ValidatorDBare used as an umbrella term for ''ligands and non-standard residues'' covers . Therefore, all properties of ligands and non-standard residues containing 7 or more 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''.
Within the 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'MotiveValidator'. These are denoted as '' environment, a ''motifmolecules relevant for validation'' is generally a fragment of a biomacromolecule, biomacromolecular complex or ligand, made up of one or more residues or parts of residues. A simply ''motifmolecules'' can in principle be any fragment of a biomolecule. Nonetheless, '''MotiveValidator''' is focused The reason [[ValidatorDB:UserManual | ValidatorDB]] focuses on the validation these types 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 molecules is that the terms ''fragment'' they exhibit high diversity and ''motif'' are used as synonyms nontriviality in this manualtheir structure.
=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 both by [[MotiveValidator:UserManual | MotiveValidator]] and [[ValidatorDB:UserManual | ValidatorDB]] is the wwPDB Chemical Component Dictionary (wwPDB CCD)<ref name="Sen_2014"/>.
=Motif=Only input Input motif or validated motif (=validated molecule)With respect to the chemistry of biomolecules, the 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 here as 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. NonethelessSpecifically, '''MotiveValidator''' is focused on the validation of residues, thus here term ''input motif'' generally refers to a fragment made up from the residue under studyindividual molecule being validated, together with its surroundings (i.e., atoms from neighboring residues, within two bonds of any atom of the validated molecule). Note that Each ''input motif'' is assigned a unique motif identifier during the terms validation based on its PDB entry of origin. On the other hand, the term ''fragmentvalidated motif'' (or '' and validated molecule'') refers strictly to the subset of atoms in the ''input motif'' are used as synonyms which were successfully mapped to atoms in this manualthe ''model''.
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 '''Continue with reading about the term model residue ([[ValidatorDB:Principles | ValidatorDB principles]], [[MotiveValidator:Principles | MotiveValidator functionality]], or simply model) to refer to a particular structure that is known return to be correct. This structure will then be used as reference template in the validation process[[ValidatorDB:UserManual | ValidatorDB]], whereby a query residue with the same name (3-letter code) as the model will be compared to the modelor [[MotiveValidator:UserManual | MotiveValidator]] manuals. 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="ligandexpoSen_2014">FengSen,ZS., Young,J., Berrisford,J.M., Chen,LM., Conroy,M.J., Dutta,S., MaddulaDi Costanzo,HL., AkcanGao,OG., OughtredGhosh,RS., BermanHudson,HB.MP. and Westbrook,Jet al. (20042014) [http://dx.doi.org/10.1093/bioinformaticsdatabase/bth214 Ligand Depot: a data warehouse bau116 Small molecule annotation for ligands bound to macromoleculesthe Protein Data Bank]. BioinformaticsDatabase (Oxford)., 202014, 2153–51–11.</ref>
</references>

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