MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
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 National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
Radka Svobodová
RS
Vařeková
CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.
Deepti
D
Jaiswal
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.
David
D
Sehnal
CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.
Crina-Maria
CM
Ionescu
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.
Stanislav
S
Geidl
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.
Lukáš
L
Pravda
Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic.
Vladimír
V
Horský
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 michaw@chemi.muni.cz.
Michaela
M
Wimmerová
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 Jaroslav.Koca@ceitec.muni.cz.
Jaroslav
J
Koča
D000117:Acetylglucosamine / Q000737:chemistry; D001665:Binding Sites; D019826:Cholic Acid / Q000737:chemistry; D036389:Ephrin-B3 / Q000737:chemistry; D006023:Glycoproteins / Q000737:chemistry; D020407:Internet; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry; D012984:Software
D036389:Ephrin-B3; D006023:Glycoproteins; D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins; D019826:Cholic Acid; D000117:Acetylglucosamine