One feature that makes MotiveValidator very efficient is that it allows the validation of multiple residues in multiple files in a single run. If you need to validate more than one residue at a time, simply request to retrieve several models from PDBeChem by specifying a list of 3-letter codes separated by commas. Alternatively, you may upload more files with model residues in a .zip archive. You may also wish to validate a residue in more than one biomolecule, in which case simply upload a .zip archive of all your input structures, or request to retrieve several structures from the Protein Data Bank by specifying a list of 4-letter PDB IDs separated by commas. Thousands of biomolecules can be scanned at a time.
Remember that the term residue refers here to any collection of atoms bound by chemical bonds (covalent, coordinative or ionic), as long as all the atoms have the same residue name (3-letter code) and residue identifier (index internal to the input PDB file). Therefore any set of atoms that can be defined as a residue (or ligand) within the MotiveValidator environment can be validated using Residue Validation. MotiveValidator will first read in the model file and establish the residue name and structural information for all its atoms. MotiveValidator will then scan the entire input biomolecule and extract all instances of residues with the same name (3-letter code) as the model. Each of these instances will be considered a separate motif, receive a unique motif identifier and subsequently be validated against the structure of the model residue.
Sugar validation is a special case of residue validation where the residues to be validated are carbohydrates. This special analysis mode allows MotiveValidator to perform fully automated validations. Specifically, MotiveValidator keeps a pre-established list of sugar residues and their models from PDBeChem, containing the residue name and structural information for all atoms in each sugar residue. The consequence of this fact is that you need not provide the sugar models yourself, and need only specify the biomolecule file. MotiveValidator will automatically scan all residues in the biomolecule file, and extract all instances of all sugars based on residue names and residue identifiers. Each instance of each sugar will be considered a separate motif, receive a unique motif identifier and subsequently be validated against its corresponding sugar model. All sugar validations take place in a single run, making sugar validation very efficient.
Try PatternQuery service for the extraction of molecular motifs.
The third type of validation that can be performed using MotiveValidator can be initiated via the Motif/Fragment Validation tab on the submission page. The Motif/Fragment Validation tab provides a brief description of the validation process, and several options for input file submission.
Remember that the term motif refers here to a fragment of a biomolecule or ligand, made up of one or more residues or parts of residues. Therefore, any set of atoms that can be defined as a motif within the MotiveValidator environment can be validated using Motif/Fragment Validation. MotiveValidator will first read in the model file and collect the structural information for all its atoms. MotiveValidator will then read in the motif file and assign it a unique motif identifier. Then, the entire structure of the motif as a whole is validated against the model, regardless of the residue names and identifiers in the motif file.