Structure validation has become a major issue in the structural biology community, and an essential step is checking the ligand structure. This paper introduces MotiveValidator, a web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward manner whether the ligand or residue being studied has a correct annotation (3-letter code), i.e. if it has the same topology and stereochemistry as the model ligand or residue with this annotation. If not, MotiveValidator explicitly describes the differences. MotiveValidator offers a user-friendly, interactive and platform-independent environment for validating structures obtained by any type of experiment. The results of the validation are presented in both tabular and graphical form, facilitating their interpretation. MotiveValidator can process thousands of ligands or residues in a single validation run that takes no more than a few minutes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening. MotiveValidator is freely available via the Internet at http://ncbr.muni.cz/MotiveValidator.

CEITEC Central European Institute of Technology Masaryk University Brno Kamenice 5 625 00 Brno Czech Republic

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

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

Faculty of Informatics Masaryk University Brno Botanická 68a 602 00 Brno Czech Republic

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PDBsum: Structural summaries of PDB entries

The Eighth Central European Conference "Chemistry towards Biology": Snapshot

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