15 Questions
What is cheminformatics primarily focused on?
Facilitating the collection, storage, analysis, and manipulation of large quantities of chemical data
What does a molecular graph in cheminformatics represent?
The topology of a molecule
How are acyclic molecules represented in cheminformatics?
Using trees
What is the main purpose of using generic, or Markush, structures in chemical disclosures in patents?
To encode more than one structure into a single representation
What does 'substituent variation' refer to in Markush structures?
Different substituents at a fixed position
What is the purpose of 'fragment-screening' in the search system for Markush structures?
To generate fragments common to all specific structures and those that occur at least once
What does the 'reduced graph representation' in the search system involve?
Differentiating between contiguous assemblies of carbons and heteroatoms
In the context of Markush structures, what does 'homology variation' refer to?
Terms representing chemical families
What is the purpose of the modified Ullmann algorithm in the search system for Markush structures?
To apply on a node-by-node basis
What method uses a hashing procedure to set bits to '1' in the fingerprint bitstring for any type of molecular structure?
Hashed fingerprint method
What is the role of patent databases in the context of chemical information retrieval?
They provide exclusivity in exchange for disclosure
What is the purpose of the Smallest Set of Smallest Rings (SSSR) in chemical structure searching?
To comprise the rings containing the fewest atoms in a molecule
What is the purpose of the Morgan algorithm in chemical graph representation?
Determining a canonical order of atoms in a molecular graph
How is geometrical isomerism about double bonds indicated in SMILES notation?
Using slashes
What is the purpose of hash keys in structure searching?
Retrieving information by moving the disk read mechanism directly to the location associated with the structure
Study Notes
Chemical Graph Representation and Structure Searching
- Isomorphic graphs have the same number of nodes and edges, and can be mapped to each other with equivalent nodes and edges.
- Connection tables communicate molecular graphs to and from computers, consisting of atomic numbers and bond pairs.
- Linear notation uses alphanumeric characters to encode molecular structures in a compact form.
- SMILES notation is a widely accepted linear notation, representing atoms by their atomic symbol and using upper and lower case for aliphatic and aromatic atoms.
- Geometrical isomerism about double bonds is indicated using slashes in SMILES notation.
- Canonical representation of molecular structures is crucial for avoiding duplicates in chemical database systems.
- The Morgan algorithm is a widely used method for determining a canonical order of atoms in a molecular graph, incorporating stereochemistry information.
- The CANGEN algorithm generates a unique SMILES string for each molecule using similar principles to the Morgan algorithm.
- Other formats for general utility include the canonical InChI representation by IUPAC and the Chemical Markup Language (CML).
- Structure searching converts the structure into a representation, allowing direct retrieval of information from the database through the generation of a hash key.
- Hash keys are integers used to retrieve information by moving the disk read mechanism directly to the location associated with the structure.
- Substructure searching identifies all molecules in the database containing a specified substructure, such as a particular functional group.
Test your knowledge of chemical graph representation and structure searching with this quiz. Explore topics such as isomorphic graphs, connection tables, linear notation, SMILES notation, canonical representation, algorithms for canonical order determination, and structure searching techniques.
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