ValidatorDB:Terminology

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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 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[1], 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

  1. Feng,Z., Chen,L., Maddula,H., Akcan,O., Oughtred,R., Berman,H.M. and Westbrook,J. (2004) Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics, 20, 2153–5.