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ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

Sehnal D, Svobodová Vařeková R, Pravda L, Ionescu CM, Geidl S, Horský V, Jaiswal D, Wimmerová M, Koča J - Nucleic Acids Res. (2014)

Bottom Line: Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules.All results are systematically classified into categories, and statistical evaluations are performed.In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries.

View Article: PubMed Central - PubMed

Affiliation: CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic.

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Examples of results provided by different validation analyses. ValidatorDB classifies results into three main categories (Completeness, Chirality, Advanced), each referring to several related analyses. Information about the source of the particular molecules displayed here is given in Supplemental Table S3.
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Figure 1: Examples of results provided by different validation analyses. ValidatorDB classifies results into three main categories (Completeness, Chirality, Advanced), each referring to several related analyses. Information about the source of the particular molecules displayed here is given in Supplemental Table S3.

Mentions: As ValidatorDB implements the approach of validation of annotation, each validated molecule is compared against a model with the same annotation from wwPDB CCD. The validation analyses performed by ValidatorDB cover the main issues which have been observed in the topology (2D structure) and geometry (3D structure) of ligands and non-standard residues, and which are important for their correct annotation. These validation analyses, along with their respective results, can be classified into three categories, namely, Completeness, Chirality and Advanced analyses (Figure 1). If no issues are found during these analyses, the molecule is marked as having complete structure and correct chirality (Figure 1a).


ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

Sehnal D, Svobodová Vařeková R, Pravda L, Ionescu CM, Geidl S, Horský V, Jaiswal D, Wimmerová M, Koča J - Nucleic Acids Res. (2014)

Examples of results provided by different validation analyses. ValidatorDB classifies results into three main categories (Completeness, Chirality, Advanced), each referring to several related analyses. Information about the source of the particular molecules displayed here is given in Supplemental Table S3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383933&req=5

Figure 1: Examples of results provided by different validation analyses. ValidatorDB classifies results into three main categories (Completeness, Chirality, Advanced), each referring to several related analyses. Information about the source of the particular molecules displayed here is given in Supplemental Table S3.
Mentions: As ValidatorDB implements the approach of validation of annotation, each validated molecule is compared against a model with the same annotation from wwPDB CCD. The validation analyses performed by ValidatorDB cover the main issues which have been observed in the topology (2D structure) and geometry (3D structure) of ligands and non-standard residues, and which are important for their correct annotation. These validation analyses, along with their respective results, can be classified into three categories, namely, Completeness, Chirality and Advanced analyses (Figure 1). If no issues are found during these analyses, the molecule is marked as having complete structure and correct chirality (Figure 1a).

Bottom Line: Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules.All results are systematically classified into categories, and statistical evaluations are performed.In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries.

View Article: PubMed Central - PubMed

Affiliation: CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic.

Show MeSH
Related in: MedlinePlus