MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

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Authors

SVOBODOVÁ VAŘEKOVÁ Radka JAISWAL Deepti SEHNAL David IONESCU Crina-Maria GEIDL Stanislav PRAVDA Lukáš HORSKÝ Vladimír WIMMEROVÁ Michaela KOČA Jaroslav

Year of publication 2014
Type Article in Periodical
Magazine / Source Nucleic Acids Research
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://nar.oxfordjournals.org/content/early/2014/05/21/nar.gku426.full.pdf+html
Doi http://dx.doi.org/10.1093/nar/gku426
Field Biochemistry
Keywords PROTEIN DATA-BANK; CRYSTAL-STRUCTURES; CRYSTALLOGRAPHY; INFORMATION; REFINEMENT; BIOLOGY; ARCHIVE; SERVER
Attached files
Description 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.
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