Universitat Rovira i Virgili

Bioinformatic Tools and Databases Developed

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VHELIBS
Author: Adrià Ceretó

http://urvnutrigenomica-ctns.github.io/VHELIBS/

Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G. (2013). The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. J Cheminform., 5(1):36. doi: 10.1186/1758-2946-5-36

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.

 

DecoyFinder
Author: Adrià Ceretó

http://urvnutrigenomica-ctns.github.io/DecoyFinder/

Cereto-Massague, A., Guasch, L., Valls, C., Mulero, M., Pujadas, G., & Garcia-Vallve, S. (2012). DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. Bioinformatics, 28(12):1661-1662. doi:10.1093/bioinformatics/bts249

DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.