VHELIBS

Validation HElper for LIgands and Binding Sites

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The Validation HElper for LIgands and Binding Sites (VHELIBS) aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e. users with little or no crystallography knowledge) by checking how their coordinates fit to their corresponding electron density map and letting the user to use models from either the PDB or PDB_REDO. The user can specify threshold values for a series of properties related with coordinates to electron density fitting (where Real Space R, Real Space Correlation Coefficient and average occupancy are the ones used by default) and, VHELIBS will automatically label residues and ligands with values within the specified limits, and the rest as either dubious or bad based on an user-configurable tolerance value. The user then is able to visually check the fitness quality of the residues/ligands to their corresponding electron density map, and reclassify them if needed.

VHELIBS aims to enable non-crystallographers and users with little or no crystallography knowledge to easily validate and use reliable structures in drug discovery and development. To that end, it features a Graphical User Interface (GUI) which makes it easy to tune the parameters for more advanced users, but also comes with carefully chosen default values that are valid for most situations.

A brief tutorial and documentation can be found in the wiki.

VHELIBS is available under the GNU Affero GPL license, which can be read here.

For any question or problem regarding VHELIBS, feel free to open an issue here about it.

Universitat Rovira i VirgiliCTNS