Editing MotiveValidator (section)

=Functionality=

[[Image:MV_manual_figures2.png|thumb|right|400px|'''MotiveValidator''' identifies the validated residue in the input structure based on the name (3-letter code) of the model residue. Then it extracts the validated residue in the form of an input motif, containing all the atoms of the validated residue, together with all atoms found within one or two bonds of any atom from the validated residue (surroundings). The validated motif results as the subset of atoms in the input motif which correspond to atoms in the model residue]]
We have developed '''MotiveValidator'''<ref name="Varekova_2014"/>, a user-friendly, interactive and platform independent environment for the speedy validation of ligands, residues and fragments (denoted as structural motifs). '''MotiveValidator''' covers all standard and custom residues and ligands, and was successfully tested in six research labs on more than 50.000 input samples.

The main purpose of the software is to help you determine whether a residue, ligand, or fragment in a biomolecule or biomolecular complex is structurally complete and correctly annotated. Specifically,  '''MotiveValidator''' checks if the topology and chirality are correct. Validation is performed against model residues from the  wwPDB chemical component dictionary.  '''MotiveValidator''' covers  all  residues  and  ligands  accessible  via  LigandExpo<ref name="Feng_2004"/>.

Additionally, you may upload your own custom model in case the residue, ligand or fragment of your interest does not have any model available in LigandExpo. However, please note that the user bears all responsibility for the correctness of uploaded models.

In its most basic form, the function of '''MotiveValidator''' is to take a residue and validate it by comparing its structure against the structure of a model residue that shares the same name (3-letter code) with the residue of interest, as you can see in the picture below. Therefore,  '''MotiveValidator''' generally requires two input  files,  namely  a  file  containing  the  residue  to  be  validated  (input  structure),  and  a  file containing the  model to be used as reference. Note that, most commonly, the input structure containing the validated residue actually includes entire biomolecules (or their fragments) and other ligands. For this reason, the interface of  '''MotiveValidator''' in fact uses the term biomolecule to refer to the input file containing  validated residues. This simply means that you need not extract the validated residue yourself before you can validate it. '''MotiveValidator''' will do that for you.

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