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A short description of SPILLO-PBSS
SPILLO-Potential Binding Sites Searcher (SPILLO-PBSS) is an innovative software purposely designed to identify target and off-target proteins of any small molecule (e.g., a drug) within very large protein structural databases (e.g., the whole available human structural proteome).
SPILLO-PBSS is able to identify targets and off-targets with no sequence nor structural homology to the main target of the small-molecule, even when the potential binding sites are strongly distorted (e.g., completely closed, buried, occupied) compared to a conformation suitable for the binding.
Such a unique feature allows SPILLO-PBSS to overcome the main drawback of traditional approaches, which are liable to miss, for example, off-target proteins responsible for adverse effects of a drug, whenever their binding sites are not already in a suitable conformation for the binding event (see Table 2 of the reference paper for a comparison with other related available methods).
A list of the potential target and off-target proteins of the drug is then provided by the software, along with many structural details concerning their potential binding sites.
- Fast identification of target and off-target proteins of a drug on a proteome-wide scale
- Identification of target and off-target proteins with no sequence nor structural homology to the main target of the drug
- Innnovative flexible structure-based approach
- Prediction and clarification of drug adverse off-target effects at biomolecular level
- Identification of targets involved in polypharmacological effects of a drug
- Identification of targets useful for new indications of a drug (Drug repositioning)
- Reduction/optimization of animal testing (according to the 3Rs principle)
- Ability of identifying drug binding sites even if strongly distorted or completely closed
- Totally unbiased search for drug binding sites in protein structures, including both surface and inner regions
Advantages over other existing tools
- Higher probability of success (POS) in drug targets and off-targets identification on a proteome-wide scale
- Superior ability in identifying potential drug binding sites even if strongly distorted compared to a suitable conformation for the binding
Experimental validations [LINK]
 A. Di Domizio et al., SPILLO-PBSS: Detecting Hidden Binding Sites within Protein 3D-Structures Through a Flexible Structure-Based Approach. J. Comput. Chem. (2014); DOI: 10.1002/jcc.23714