ArticleJournal of cheminformatics2013
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites.
Article in Journal of cheminformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Avoiding pitfalls when modelling ligands in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- Halogen bonds between ligands and proteins: Can we use them in validation?Protein science : a publication of the Protein Society · 2025Article
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening.Molecules (Basel, Switzerland) · 2021Article
- 'International journal of molecular sciences · 2021Article
- Crystallographic models of SARS-CoV-2 3CLIUCrJ · 2021Article
- The Light and Dark Sides of Virtual Screening: What Is There to Know?International journal of molecular sciences · 2019Review
- Article
- Detect, correct, retract: How to manage incorrect structural models.The FEBS journal · 2018Review
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
- Tools for ligand validation in Coot.Acta crystallographica. Section D, Structural biology · 2017Article
- Open source molecular modeling.Journal of molecular graphics & modelling · 2016Review
- Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.Acta crystallographica. Section D, Structural biology · 2016Article
- Models of protein-ligand crystal structures: trust, but verify.Journal of computer-aided molecular design · 2015Article
- MTiOpenScreen: a web server for structure-based virtual screening.Nucleic acids research · 2015Article
- The solvent component of macromolecular crystals.Acta crystallographica. Section D, Biological crystallography · 2015Review
- You are lost without a map: Navigating the sea of protein structures.Biochimica et biophysica acta · 2015Review
- A series of PDB-related databanks for everyday needs.Nucleic acids research · 2015Article
- Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design.Molecules (Basel, Switzerland) · 2014Review
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB.
resultsThe Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.
conclusionsVHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments.
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