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As an input, the VoroMQA server accepts one or more structures (models) in PDB format. Input structures can contain multiple chains, biological assemblies are also accepted. User can provide a sequence to filter and renumber the residues in the submitted PDB files. User can also enable the evaluation of inter-chain interface in addition to the whole structure assessment.
As an output, the server provides global scores, local (per-residue) scores, and additional local context information on secondary structure and solvent accessibility. Moreover, if the evaluation of inter-chain interactions was requested, the server provides interface quality scores, interface energy estimates, and local scores for residues involved in inter-chain interfaces.
All the local scores are presented in forms of interactive (clickable) plots and interactive color-coded scoring profiles and 3D structures. Various visualizations can be turned off and on, allowing a user to focus on some of the features without being distracted by the others, which is particularly useful when viewing results for multiple models on a single page. The VoroMQA server also provides an interactive plot for viewing and interpreting global scores of multiple models.
Almost every page contains a "Show help" button. It can be clicked to view the appropriate instructions and hints for the page.