MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).

The applications provided within the MotiveValidator platform cover all residues and ligands defined in the wwPDB CCD, and available via PDBeChem. In addition, you may specify your own model residue if it is not available in wwPDB CCD.

× Are you interested in validating ligands and non-standard residues in existing PDBe.org entries? Check out ValidatorDB.
  • Click on each of the application tabs to read about the functionality of a specific MotiveValidator application, and upload the structures you wish to study. If you do not have any input PDB or PDBx/mmCIF files ready or are unsure regarding what the input files can look like, just view the results to one of our sample calculations. You will be able to download sample input files from there.
  • Note that some of the applications work with the structure of entire biomolecules, whereas other applications work with fragments of these structures.
  • Once your calculation is complete, you will be redirected to a results page, where you will be able to analyze your results in detail, both statistically and visually.
  • You will be provided with a link to your results page, so that you can return, analyze or download your results later. The results page address is not publicly visible.
  • For a step-by-step guide about how to work with MotiveValidator and how to analyze your results, see the Manual. Should you have any further questions or comments, feel free to contact us at david.sehnalmail.muni.cz.
  • For a quick demo, view the Tutorial and examine the results of our calculations.
    Proteins with CHD
    This case study illustrates the basic structural analysis of residues or ligands using Residue Validation. The analysis allows to extract and explicitly log the structural problems in each of almost 300 instances of cholic acid (CHD) that appears as a ligand with over 50 protein structures. Note that more than one residue can be validated at a time, either by uploading several model residues, or by specifying more residue names in the PDBeChem search bar.
    Lectins with MAN
    This case study illustrates a fully automatic analysis of lectins using Sugar Validation. Lectins are proteins involved in biological recognition. This analysis allows to quickly identify, sort and validate all carbohydrates that can be found cocrystalized with α-D-mannose (MAN) ligands in lectins.
    Complexed Glycoprotein (3D12)
    This case study illustrates a fully automatic analysis of multiple carbohydrates in a single structure (PDB ID 3D12) using Sugar Validation. This task is challenging from the validation point of view because the complex of the Nipah G attachment glycoprotein and its receptor ephrin B contains 30 ligands, originating from 11 different carbohydrates.
    MAN Motifs
    This case study illustrates a Motif/Fragment Validation analysis for a very large set of structures containing α-D-mannose (MAN) residues occurring in Protein Data Bank (snapshot from January 9th 2014). Note that each motif contains not only a MAN residue, but also any atoms that were found bound to the MAN residue via one or two bonds in the input structure. This analysis is very efficient at quickly identifying and logging structural problems in large data sets, such as all instances of MAN in the Protein Data Bank.
    NAG Motifs
    This case study illustrates a Motif/Fragment Validation analysis for a very large set of structures containing N-acetyl-D-glucosamine (NAG) residues occurring in the Protein Data Bank (snapshot from January 9th 2014). NAG is the second most common ligand in the Protein Data Bank, amounting to more than 23 000 instances of NAG in almost 4000 protein structures (almost 5 times the number of MAN motifs). This analysis shows all possible types of errors and warnings that can be reported by MotiveValidator.
    BCL Motifs
    This case study illustrates a Motif/Fragment Validation analysis for a set of structures containing bacteriochlorophyll a (BCL) residues occurring in Protein Data Bank (snapshot from January 9th 2014). BCL is a very complex ligand with many chiral centres. A BCL residue includes a Mg ion, several adjacent rings and a long hydrocarbon side chain. Note that each motif contains not only a BCL residue, but also any atoms that were found bound to the BCL residue via one or two bonds in the input structure. This analysis allows to study all parts of the BCL structure in detail in all cases.
  • If you found MotiveValidator helpful, please cite:
    Svobodová Vařeková, R., Jaiswal, D., Sehnal, D., Ionescu, C.-M., Geidl, S., Pravda, L., Horský, V., Wimmerová, M. and Koča, J.: MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res., 42, W227–33 (2014).

Automatic sugar validation in one or more biomolecules

  • Reads the entire structure of an input biomolecule or biomolecular complex, automatically detects all sugar (carbohydrate) residues present, and subsequently validates them with respect to model residues obtained from the wwPDB Chemical Component Dictionary.
  • The structure of each sugar residue in the input structure is compared with the wwPDB Chemical Component Dictionary model residue that has the same annotation, i.e., the same 3-letter residue name according to PDB standards.

From File
Select fileChange Remove
Select a single file or a ZIP file containing entire biomolecule(s) in PDB or PDBx/mmCIF format (300MB limit).
From PDBe.org
PDB identifiers are used only if no file is selected. Loaded from PDBx/mmCIF format.

Automatic custom residue validation in one or more biomolecules

  • Reads the structure of an input biomolecule or biomolecular complex, and an input model residue to serve as reference template for validation.
  • Scans the entire biomolecule(s), automatically detects all residues in the input biomolecule(s) with the same annotation (i.e., the same 3-letter code) as the model residue, and subsequently validates them by comparison to the model.

From wwPDB CCD
To validate more residues or ligands in one run, enter a comma separated list of 3-letter codes.
From File
Select fileChange Remove
Select a single file or a ZIP file containing model residues(s) (a model must contain exactly one residue) in PDB or PDBx/mmCIF format.
When using the PDB format, it is recommended that the input is a ZIP archive with both PDB and SD/SDF/MOL (for bonds) versions present.
From File
Select fileChange Remove
Select a single file or a ZIP file containing entire biomolecule(s) in PDB or PDBx/mmCIF format (300MB limit).
From PDBe.org
PDB identifiers are used only if no file is selected. Loaded from PDBx/mmCIF format.

Validation of precomputed structural motifs against a model residue

  • Reads the structure of an input structural motif (residue or fragments of residues) or a set of motifs, and an input model residue to serve as reference for validation.
  • Validates each structural motif by comparison to the model residue, regardless of the annotations (i.e., the entire structure of each motif as a whole will be validated against the model residue).
  • To extract your own fragments/motifs, you can download the MotifExtractor utility from the Command Line Version tab.

From wwPDB CCD
From File
Select fileChange Remove
Select a PDB or PDBx/mmCIF file containing your model residue (a model must contain exactly one residue).
When using the PDB format, it is recommended that the input is a ZIP archive with both PDB and SD/SDF/MOL (for bonds) versions present.
From File
Select fileChange Remove
Select a single file or a ZIP file containing motif(s) in PDB or PDBx/mmCIF format (300MB limit).

Command line version of the MotiveValidator service

The command line version provides access to the underlying service. For usage instructions, please consult the Wiki page.
Current Version (1.1.15.8.8e)
All Versions (change log): Download

MotifExtrator
To extract your own fragments/motifs, you can use MotifExtractor, a simple automated script for extracting the motifs of interest from biomolecule structure files. For usage instructions, please consult the Wiki page.

Database mirrors last updated 6/23/2016. wwPDB CCD with 21898 ligands (view all, sugars), PDB with 119823 structures.
Service version 1.1.15.8.8e (change log).