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| The advancement of research in structural biology has provided a large body of structural data deposited in various databases. One great example is the Protein Data Bank (PDB), which has been growing exponentially, and which currently consists of more than 100,000 structures of biomolecules and their complexes. Such large bodies of data, especially accumulated over a short period of time using high throughput techniques, will inherently be plagued by various problems. Validation arose as a major issue in the structural biology community when it became apparent that some published structures contained serious errors, either documented (e.g., due to insufficient electron density in a certain area), or not. Structural databases generally require that the new
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| submissions be checked prior to acceptance. The tools employed for presubmission validations work fairly well for well studied residues like amino acids or nucleotides. However, an essential step in the validation process is checking the ligand structure, because ligands play a key role in protein function, and also because they are the main source of errors in structures. Ligand validation, as well as the validation of uncommon residues, are very challenging tasks, because of the high diversity and nontriviality of their structure, and the general lack of information about correct structures. Therefore, software tools focused on ligand validation were developed relatively recently, and the topic is still under active development. These tools are able to validate one or more structures (even thousands of structures), but they are not able to provide the broad scientific community with a more complex image of the quality of structures in dedicated and well established structural databases. For example, a general overview and corresponding statistical evaluation of validation results for residues and ligands in the entire PDB is not yet available, despite the exponential growth of the PDB and the development of structural validation tools in recent years.
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| We had recently developed MotiveValidator, an interactive platform for the speedy validation of ligands, residues and fragments using a novel, straightforward approach based on the validation of residue annotation.
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| MotiveValidator employs advanced algorithms for the detection and comparison of structural motifs, along with tools for chirality verification and interactive visualization of 3D structures. Using MotiveValidator, we further created ValidatorDB, a comprehensive resource of validation results for residues and ligands in the Protein Data Bank. Along with validation results for individual residues and ligands, ValidatorDB also provides a summary and statistical evaluation of the validation results at various levels of detail within the PDB. Thus, ValidatorDB offers a comprehensive overview of the quality of the ligand structures in the entire PDB.
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| ==Availability and technical details==
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| {{TopicTOC-Availability}}
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| {{Main|Availability (word)}}
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| Where to find
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| Validator
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| DB
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| Validator
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| DB
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| is freely available via the internet since May 2014 at
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| http://ncbr.muni.cz/MotiveValidatorDB. There is no login requirement for accessing Validator DB.
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