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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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Detailed validation report for the saccharide MAN 957 from PDB entry 1E4M. The structure is complete, but exhibits a chirality error on atom C5. Additionally, the warning of foreign atom at position O1 indicates that this molecule is part of an oligosaccharide chain.
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Figure 2: Detailed validation report for the saccharide MAN 957 from PDB entry 1E4M. The structure is complete, but exhibits a chirality error on atom C5. Additionally, the warning of foreign atom at position O1 indicates that this molecule is part of an oligosaccharide chain.

Mentions: Validation report for a particular molecule or a set of molecules (accessible via Search → Molecule Identifier), depicted in Figure 2.


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)

Detailed validation report for the saccharide MAN 957 from PDB entry 1E4M. The structure is complete, but exhibits a chirality error on atom C5. Additionally, the warning of foreign atom at position O1 indicates that this molecule is part of an oligosaccharide chain.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Detailed validation report for the saccharide MAN 957 from PDB entry 1E4M. The structure is complete, but exhibits a chirality error on atom C5. Additionally, the warning of foreign atom at position O1 indicates that this molecule is part of an oligosaccharide chain.
Mentions: Validation report for a particular molecule or a set of molecules (accessible via Search → Molecule Identifier), depicted in Figure 2.

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