Ligand-based Pharmacophore Model Service


Ligand-based Pharmacophore Model Service

In drug discovery, the receptor structure is often unknown, but the ligand structure is known. If only a single active molecule is known, it is impossible to map the key contributing pharmacophore characteristics to the molecule, and the only option may be to use similarity queries (eg, using pharmacophore fingerprints) to retrieve similar molecules. When active ligands with a set of different skeletons of known structure are available, ligand-based pharmacophore modeling can be used. The clarification of the pharmacophore involves two steps. First, the conformational space of flexible molecules needs to be widely covered because the biologically active conformation is unknown. Second, the molecules need to be compared by common pharmacophore characteristics, which can be retained in the 3D model.


Ligandscout is a professional pharmacophore modeling and virtual screening tool. In addition to structure-based design, it is also good at ligand-based design: starting from a series of compounds with similar binding patterns to identify and identify pharmacophore models. The input file of Ligandscout contains: training set compounds (active compounds, inactive compounds) and test set compounds (active compounds, inactive compounds), training set compounds are used to generate pharmacophore models, test set compounds continue to multi-pharmacophore models scoring, and finally output up to 10 models with scoring.

Ligand-based Pharmacophore Model Service 1

Our Ligand-based pharmacophore modeling service

Project Name Ligand-based Pharmacophore Modeling Service
Samples requirement Our ligand-based pharmacophore modeling service requires you to provide specific drug construction requirements.
Timeline Decide according to your needs.
Deliverables We provide you with raw data and calculation result analysis service.
Price Inquiry

Process ligand-based pharmacophore model service

  • Import ligands and set up training set compounds

Ligand-based Pharmacophore Model Service 2

  • Set Training Set Compound

Ligand-based Pharmacophore Model Service 3

  • Cluster the training set according to the characteristics of the 3D pharmacophore
  • Set up test set compounds
  • Ligand-based pharmacophore model

Ligand-based Pharmacophore Model Service 4

  • Virtual screening and preservation of pharmacophore models

Virtual screening and preservation of pharmacophore models


  • The active compounds in the training set are used to generate all possible public pharmacophore models.
  • The inactive compounds in the training set are used to score the model generated in the first step: the model hit by the inactive compounds gets worse.
  • The model is further scored with the active compound/non-active test set: the model that matches the active compound is scored, and the score that is not matched is deducted; the score is matched with the inactive compound, and the score is not matched.
  • The models are sorted according to the score value, and the 10 models with the highest scores are retained.

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