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Pharmacophore Modeling and Screening


The pharmacophore is an active conformation that generates geometric and energy matching with the target when the drug molecule interacts with the receptor target. In recent years, with the development of compound databases and computer technology, virtual screening using pharmacophore models has been widely applied. As one of the important methods for discovering lead compounds, pharmacophore modeling is established based on the characteristic elements of pharmacodynamics, presenting the structural characteristics that play a key role in the activity. Pharmacophore modeling and screening is a powerful tool that can generate and use 3D structures to search for novel active compounds, especially when there is a lack of receptor structure information.

3D Pharmacophore-based virtual screening workflow.Figure 1. 3D Pharmacophore-based virtual screening workflow. (Seidel, T.; et al. 2010)


  • Study the interaction between the ligand (drug molecule) and its receptor (known target protein or active site).
  • Predict the binding mode and affinity.
  • Discover and optimize drug lead molecules.
  • Predict ADMET to determine the possible interactions between drugs and drug-metabolizing enzymes.

Our Methodologies

  • Pharmacophore query based on 'receptor-ligand' interaction

A 3D pharmacophore query model is constructed based on the structure of the complex. We use the pharmacophore query method to filter the conformation database to identify the active compound candidates. Boolean expressions of drug efficacy characteristics and various shape constraints are applied in our pharmacophore query method. Moreover, we also apply SMARTS approaches to optimize the query.

  • Consensus pharmacophore modeling based on the structure superposition of active compounds

The pharmacophore is constructed based on a batch of suerimposed active compounds and the consensus pharmacophore is determined based on the tolerance radius, conservative scoring threshold, and conservative credit scoring. At Alfa Chemistry, our experts mainly apply this method to the modeling of highly active molecules.

  • Automatic pharmacophore modeling based on activity data of large batches of compounds

For compounds with known activity data, each pharmacophore will be scored according to the known active compounds, statistically active molecules, and the degree of atomic superposition in conformation matching. The molecular superposition results corresponding to high-scoring pharmacophores will be further analyzed. Our scientists fully consider all possible combinations of pharmacodynamic characteristics, and adopt a special construction strategy to avoid repeated attempts.

  • High-throughput conformation search

Alfa Chemistry has developed a high-throughput conformation search method to construct a conformation database for virtual screening. Our method is a parallel, fragment-based method in which the fragment conformations are assembled by overlapping atoms.

  • Pharmacophore search

We can quickly search the compound conformation database to find the molecular conformation that suits the pharmacophore model. Our teams can search multiple databases at once, search for a specified range of molecules, or search for docking results. In addition, we support partial matching, stacking matching and key feature definition matching.

Modeling and Screening Process

  • Ligand and receptor structure preparation and optimization
  • Pharmacophore modeling (Based on structure/ligand/molecular field)
  • Characteristic modification of pharmacophore
  • Enrichment analysis of pharmacophore
  • Virtual screening based on pharmacophore
  • Analysis of virtual screening results based on pharmacophore modeling

Our Capabilities

  • Structure-based pharmacophore modeling
  • Ligand-based pharmacophore modeling
  • Molecular field-based pharmacophore modeling
  • Evaluation of the quality of pharmacophore modeling
  • Adjust the characteristics of the pharmacophore and the combination model
  • Use pharmacophores to score the docking conformation
  • Construct a high-quality compound conformation library

Our pharmacophore modeling and screening services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Seidel, T.; et al. Strategies for 3D pharmacophore-based virtual screening. Drug Discovery Today Technologies. 2011, 7(4): 221-228.

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