11 Questions
Which method offers a complementary alternative to substructure searching and 3D pharmacophore searching?
Similarity Searching
Advantages of Similarity Searching include:
No need to define a precise substructure or pharmacophore query
What principle supports the idea that structurally similar molecules tend to have similar properties?
Neighborhood Principle
Which similarity coefficient is commonly used for binary fingerprints such as structural keys and hashed fingerprints?
Tanimoto coefficient
What does the Tanimoto coefficient measure?
The similarity between two molecules
Which coefficients directly measure similarity?
Tanimoto and Dice coefficients
Why do smaller molecules tend to have lower similarity values when using the Tanimoto coefficient?
They naturally tend to have fewer bits set to '1'
Which geometric shapes are typically used to approximate a sphere in the SPERM program?
Icosahedrons
What is the basis for calculating the similarity between molecules in the SPERM program?
Root mean squared difference
What is the enrichment factor in similarity methods?
The ratio of actives actually received at a given rank to actives retrieved by pure chance
Which compound libraries and screening methods are used in the similarity search using the SwissSimilarity tool?
Bioactive: ChEMBL full database 2D & 3D Combined; Commercial: ZINC (Drug-like) 3D Electroshape; Synthesizable: Enamine FP2
Study Notes
Similarity Searching
- Similarity searching offers a complementary alternative to substructure searching and 3D pharmacophore searching.
Structural Similarity Principle
- The principle that structurally similar molecules tend to have similar properties supports the idea of similarity searching.
Coefficients in Similarity Searching
- The Tanimoto coefficient is a commonly used similarity coefficient for binary fingerprints such as structural keys and hashed fingerprints.
- The Tanimoto coefficient measures the similarity between two binary fingerprints.
Tanimoto Coefficient
- The Tanimoto coefficient directly measures similarity.
- Smaller molecules tend to have lower similarity values when using the Tanimoto coefficient because they have fewer bits set to 1.
SPERM Program
- The SPERM program uses geometric shapes, typically spheres or ellipsoids, to approximate a sphere.
- The basis for calculating the similarity between molecules in the SPERM program is the overlap volume of the spheres.
Enrichment Factor
- The enrichment factor in similarity methods is a measure of how well the method performs in retrieving actives.
SwissSimilarity Tool
- The SwissSimilarity tool uses compound libraries and screening methods, such as high-throughput screening (HTS) and virtual screening (VS), in similarity searches.
This quiz explores various similarity methods used in chemical compound searching, including 2D fingerprints, similarity coefficients, and other descriptor methods. It also covers the concept of 3D similarity and its relevance in pharmacophore searching. Test your knowledge and learn more about how similarity searching can be a useful tool in finding compounds similar to a query compound.
Make Your Own Quizzes and Flashcards
Convert your notes into interactive study material.
Get started for free
