Molecular Clustering Analysis Using Discovery Studio


Discovery Studio is a software application for molecular modeling and drug discovery. It provides a suite of tools to study and analyze complex biomolecular systems, including proteins, nucleic acids and other large molecules. a key feature of Discovery Studio is its ability to perform molecular clustering analysis, which can be used to identify structurally similar molecules and group them together based on their properties.

Importance of Molecular Clustering Analysis

Molecular clustering analysis can be a powerful tool for drug discovery because it allows researchers to identify compounds with similar structures and biological activities. By grouping these compounds together, researchers can gain insight into the underlying mechanisms of drug action and potentially identify new targets for drug development. In this article, we will explore the fundamentals of how molecular clustering analysis works in Discovery Studio and provide a step-by-step tutorial for performing such analysis.


One of the key features of Discovery Studio's molecular clustering analysis tool is its ability to calculate pairwise similarity scores between molecules. These similarity scores can be based on a variety of different metrics, including molecular shape, electrostatic potential, and chemical composition.

Data Format Requirements

Discovery Studio can work with a variety of file formats, including PDB, MOL, and SDF files. Once you have imported your data, you can begin exploring the molecular structure and properties of your compounds.


1. Import your molecule data into Discovery Studio

Click on Small Molecules>Design and Analyze Libraries>Cluster Ligands in the tool browser to open the Cluster Ligands dialog box.

Select the molecular libraries to be clustered in the Input Ligands option.

Note: One or more MDL MOL / SD files can be specified, and optionally all, selected or visible ligands can be specified in the active molecule window.

Molecular Clustering Analysis Using Discovery Studio

2. In the Cluster Selection option you can select the clustering method:

  • Fixed Number of Clusters: The number of clusters to be clustered
  • Fixed Number of Molecules per Cluster: Average number of molecules per cluster

3. Choose the similarity metric you want to use for clustering. For example, you might choose "Shape" or "Physicochemical Properties" as your similarity metric.

4. Select the range of similarity scores you want to use for clustering. This will determine the level of granularity in your clusters; a wider range of similarity scores will result in fewer, larger clusters, while a narrower range will result in more, smaller clusters.

5. Just click Run to run the task. When the task is completed, you can see in the table browser that the molecules are divided into different clusters.

After the results are generated, you can further explore their properties and identify potential similarities between compounds. For example, you can use the software's visualization tools to compare the 3D structures of different molecules in a given cluster, or you can use the software's database search function to find related compounds with similar structures or biological activities.

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Molecular Clustering Analysis

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