LIGEX is research software for very fast searching of 3D small molecule databases based on ligand atom types and ligand atom-atom distances.
LIGEX enables the searching of any 3D small molecule dataset. This includes:
- experimental data resources, for example, COD (Crystallographic Open Database);
- ligands from the PDB (Protein Data Bank)
- compound sets from chemical suppliers; and
- virtual datasets
With LIGEX researchers can:
- find new ligand candidates for lead discovery, eg, using database searching following automated docking of a protein substrate or transition state mimic
- find new ligand substituents for lead optimisation, eg, starting from the x-ray structure of a protein-ligand complex
- provide new templates for scaffold hopping, eg, using x-ray structure of the current development candidate to define search queries
- match existing drugs, with well understood toxicity profiles, with other targets/therapeutic indications
LIGEX is different because:
- it bases ligand atom typing on DesertSci’s proprietary ViewContacts atom SMARTS types and the favourable non-covalent interactions that are possible for each atom type. Hits based on searches using these descriptors will be novel compared to established 3D pharmacophore type searching
- the pre-defined grouping of ViewContacts atom types and noncovalent interaction types, (into sets such as polar and non-polar) is a unique feature of ViewContacts that translates into unique hitlists for LIGEX
- the focus is on searching experimental 3D ligand conformations
- the focus is on searching the small molecule x-ray crystallography database, COD, which has recently grown to become an important database resource
- the focus is on searching small molecules extracted from the PDB, with an increased emphasis on ligand 3D structure and all potential interactions available, not just those observed in the complex
- our approach of using small molecules extracted from the PDB is particularly well suited to drug re-purposing. We use novel 3D ligand conformations that are already influenced by electrostatic and hydrophobic properties in protein binding sites and by interactions with amino acid side-chains.
LIGEX is a vital tool for you because it will:
- aid the discovery of new medicines in new therapeutic areas
- find safer drugs to ones currently in trials or in the clinic
- enable the use of existing drugs with manageable side effects for
other therapeutic indications.