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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.
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 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 ''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= 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''. =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.................. =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''.