Pharmacophore Modeling



Drug Discovery Services

  • Experienced and qualified scientists functioning as project managers or study director
  • Independent quality unit assuring regulatory compliance
  • Methods validated per ICH GLP/GMP guidelines
  • Rigorous sample tracking and handling procedures to prevent mistakes
  • Controlled laboratory environment to prevent a whole new level of success

Pharmacophore Modeling


What is Pharmacophore Modeling?

Each type of atom or group in a compound exhibiting chemical properties can be recognized and simplified into a pharmacophore feature by the developed model. A pharmacophore shows the spatial arrangements of molecular features and confirms the optimal molecular interactions.

Fig.1 (A) Structure- and (B) ligand-based pharmacophore model. (Teresa, K.; et al. 2015)Fig.1 Two kinds of pharmacophore models. (Teresa, K.; et al. 2015)

Methodologies of Pharmacophore Modeling

Based on the detailed information of your project, we introduce two basic approaches to establish pharmacophore models:

  • When the structure of target is unknown, our scientists perform ligand-based pharmacophore modeling method in which we extract common chemical characteristics from 3D structures of multiple reference ligands and conduct the searching of pharmacophores that would match the active compound.
  • The structure-based pharmacophore modeling is conducted based on target-ligand complexes and generates the selected chemical features and sterical relationships. We build this model by detecting the possible molecular interaction sites.

Applications of Pharmacophore Modeling

  • We guide the molecular docking and simulation, improving the outcomes of your virtual screening with our flexible solutions.
  • The identification of the interactions of drugs with drug-metabolizing enzymes can be achieved through pharmacophore methods, which means you can conduct ADME studies and toxicity prediction.
  • Our collections of diverse models can identify the drug-like molecules that the model fits well and enable to identify the target with a unknown activity.

Our Services of Pharmacophore Modeling

  • Our scientists are capable of identifying the key pharmacophore features of bioactive molecules and build quantitative structure-activity relationships (QSAR) models based on them.
  • We have designed modern ligand alignment algorithms and machine learning algorithms with accurate pharmacophore fingerprints.
  • We develop a pharmacophore method to perform virtual screening and search for new scaffold-based compounds with similar biological activity. And we also provide the subsequent services for synthesizing novel active molecules.
  • We optimize the outcome of docking simulations by removing compounds that fail to bind according to the pharmacophore query.
  • We develop 3D pharmacophore models in the molecular dynamics computational studies to modulate bioactivity by presenting a physiologically relevant dynamic interaction pattern.
  • We perform ADME-tox prediction by matching the chemical groups of target molecules to drug molecules with known ADME-tox profiles.
  • We can perform target-fishing and provide prediction of possible side effects or off-targets, improving your outcome of target investigation.
  • Our experts use pharmacophore knowledge to give additional support for de novo drug design to assess the drug-likeness and bioactivity of the designed compounds.

Our Advantages of Pharmacophore Modeling Services

  1. BOC Sciences has multiple strategies to perform both ligand-based and structure-based pharmacophore methods depending on the type of your experiments.
  2. We are capable of offering 2D and 3D pharmacophore model buildings development.
  3. Our groups can conduct virtual screening based on pharmacophore approaches with advanced and high performance computing software.
  4. We have professional competence in the determination of the structure of targets and target-ligand complexes.


  • Teresa, K.; et al. Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases. Molecules. 2015, 20(12).

※ It should be noted that our service is only used for research.

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