Pharmacophore Model Construction Service

The pharmacophore model contains multiple functions of a specific 3D model. Each feature is usually represented as a sphere (despite changes), and the radius determines the deviation tolerance from the precise position. These functions can be marked as a single function or any logical combination of "AND," "OR," and "NOT." If a molecule can be placed in a sphere that represents the query feature, the molecule is considered a hit molecule. In general, pharmacodynamic group queries may be too complicated to find hit molecules from a given library. In this case, only certain functions that are considered essential to the activity can be matched. Adjusting molecules or facilitating molecular docking simulations are other uses of the model. Depending on the situation and the type of experiment, a variety of strategies can be used to manually build a pharmacophore model, or an automatic algorithm can be used.

Pharmacophore model.Figure 1. Pharmacophore model.

Our Pharmacophore model construction services

Project Name Pharmacophore Model Construction Service
Samples requirement Our pharmacophore model construction 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

Our Pharmacophore model construction classifications

Classifications Descriptions
  • No protein structure, no ligand structure
If the target structure and all its ligands are unknown, pharmacophore modeling is very difficult. Considering the large number of available protein structures and potential compound formulas is to better model pharmacophores in order to effectively cover the chemical space in any search process.
  • No protein structure, active ligand structure
If only a single active molecule is known, the only option may be to use similarity queries (for example, using pharmacophore fingerprints) to retrieve similar molecules.
  • The structure of proteins and ligands is known
Such structure-based pharmacophore queries have multiple applications: they can be used for virtual screening, ligand binding posture prediction, and comparison of binding sites.
  • Only protein structure
The structural information of protein receptors is known, but there is no active ligand. In this case, a putative pharmacophore model can be constructed by analyzing the chemical properties of the binding site of interest.

CD ComputaBio also provides you with

Pharmacophore Model Construction Service

  • Feasibility assessment of new drug targets.
  • High-throughput screening and active compound discovery based on structural design.
  • Discovery of active compounds to lead compounds.
  • Optimization of lead compounds to determination of preclinical drug candidates.
  • Research on structure-activity relationship.


The pharmacophore model is mainly used in three areas:

Applications of Pharmacophore Model Construction Service

  • Discover the key pharmacodynamic characteristics of drug molecules to establish a clear structure activity relationship;
  • Scaffold hopping (scaffoldhopping), a virtual screening of the compound library through the method of pharmacophore to find a new skeleton compound that is active on the target;
  • Target prediction through pharmacophores to predict the pharmacological action spectrum of compounds. By using pharmacophore models, it is possible to predict leading adverse reactions early in drug development, thereby reducing the probability of drug development failure.

Related services

CD ComputaBio is a professional and efficient team. The team has more than 40% of employees with master degree, doctor degree and above. Treating customers' projects CD ComputaBio is racing against time, mission must be reached, efficient and timely delivery of tasks, customer satisfaction and trust. If you have drug design needs, please feel free to contact us.

* For Research Use Only.