37 Questions
What is the abbreviation of CHEMICAL INFORMATICS?
Chemoinformatics
Which field uses computers and computer programs to facilitate the collection, storage, analysis, and manipulation of large quantities of chemical data?
Chemoinformatics
What are the central concepts behind cheminformatics?
Quantitative Structure–activity relationships (QSAR) and Quantitative structure-property relationship (QSPR)
What is the hierarchy of Cheminformatics and Bioinformatics Research based on?
Molecular Similarity and Chemotype Structure Interaction
What are the key components in the representation and manipulation of 2D molecular structures?
Computer Representations of Chemical Structures and Structure Searching
Which field focuses on compound property prediction and structure–activity relationships?
Cheminformatics
What does cheminformatics facilitate the handling of?
Large quantities of chemical data
What is the purpose of Beilstein Handbuch der Organischen Chemie?
To provide information for planning chemical syntheses
What is the main function of the patent system?
To confer a period of exclusivity and protection for a novel invention
What is the purpose of using generic, or Markush, structures in patents?
To encode more than one structure into a single representation
What are the main types of variation seen in Markush structures?
Substituent, position, frequency, and homology variation
What is involved in a reaction search?
Structures or substructures of the precursor or reactant, product, specific reagents, and reaction conditions
What is the purpose of SciFinder Scholar in relation to reactions?
To provide access to over 6 million reactions in the CASREACT database
What does the search system involving fragment-screening generate?
Two sets of fragments: those common to all specific structures and those occurring at least once
What is the main function of the ChemDraw drawing tool in relation to Lagundi compounds?
To generate the SMILES string and the InChI representation of each compound
What is the top 1 hit in a substructure search in PubChem using the bioactive substance for cough and asthma as the query molecule?
This information is not provided in the given text
What is the purpose of the canonical SMILES algorithm?
To produce a canonical ordering of atoms in a graph
What is the purpose of substructure searching?
To identify molecules containing a specified substructure
How are graph theoretic methods used in substructure isomorphism screening?
To rapidly eliminate non-matching molecules from the database
What is the purpose of using bitstrings in substructure screening?
To represent the query substructure and database molecules for screening
What is the role of the Ullmann algorithm in subgraph isomorphism?
Uses adjacency matrices to represent molecular graphs
What is the purpose of using MDL connection table and SMARTS?
To specify substructure-related information
What is the benefit of identifying the Smallest Set of Smallest Rings (SSSR)?
Helps in classifying ring systems in complex molecules
What do nodes in a molecular graph represent?
Atoms
What is the purpose of linear notations like SMILES?
To store and transmit large numbers of molecules
What is the main function of the Morgan algorithm?
To establish a unique ordering of atoms for a given molecular graph
How are stereochemistry and geometrical isomerism indicated in SMILES notation?
Using specific symbols and notations
What is the purpose of connection tables in communicating the molecular graph to and from the computer?
To provide atomic numbers and bond pairs
What is the key feature of a tree in graph theory?
It has a single path connecting each pair of vertices
What is the role of the CANGEN algorithm?
To generate a unique SMILES string for each molecule
What is a molecular graph?
A graph representing the topology of a molecule with nodes as atoms and edges as bonds.
What is a subgraph in the context of molecular graphs?
A subset of nodes and edges of a graph.
What is a tree in the context of molecular graphs?
A special type of graph with a single path connecting each pair of vertices and no cycles or rings.
What is a connection table in the context of molecular structures?
A means to communicate the molecular graph to and from the computer, consisting of atomic numbers and bonds.
What is the Simplified Molecular Input Line Entry Specification (SMILES) notation used for?
Encoding the molecular structure using alphanumeric characters for compact representation.
How are double bonds represented in SMILES notation?
Using '=' and triple bonds using '#'; single and aromatic bonds are not explicitly represented.
What is the purpose of the Morgan algorithm in the context of molecular structures?
Determining a canonical order of the atoms for a given molecular graph.
Study Notes
Structure Searching and Substructure Screening Methods
- The canonical SMILES algorithm produces a canonical ordering of atoms in a graph, similar to the Morgan algorithm.
- Formats like canonical InChI representation and Chemical Markup Language are designed for general utility.
- Structure searching converts the structure into a representation and generates a hash key to retrieve information from a database.
- Substructure searching identifies molecules containing a specified substructure, such as a functional group.
- Graph theoretic methods are used for substructure isomorphism screening to rapidly eliminate non-matching molecules from the database.
- Bitstrings are used to represent the query substructure and database molecules for screening.
- Screening methods use a structural key, hashed fingerprint, and predefined fragment dictionary for substructure screening.
- Hashed fingerprint does not require a predefined fragment dictionary and is applicable to any molecular structure.
- The Ullmann algorithm uses adjacency matrices to represent molecular graphs for subgraph isomorphism.
- Modern substructure search methods enable complex queries, such as specifying atoms as part of a group or excluding specific atoms.
- MDL connection table and SMARTS are used to specify substructure-related information.
- Identifying the Smallest Set of Smallest Rings (SSSR) helps in classifying ring systems in complex molecules.
Computer Representations of Chemical Structures
- Chemical structures are stored in a computer as molecular graphs, which consist of nodes (atoms) connected by edges (bonds).
- Nodes in a molecular graph correspond to atoms and edges to bonds, with associated properties like atom type and bond order.
- Subgraphs are subsets of nodes and edges of a graph, for instance, the graph of Benzene is a subgraph of Aspirin.
- A tree is a special type of graph with a single path connecting each pair of vertices and is used to represent acyclic molecules.
- Isomorphic graphs have the same number of nodes and edges and can be established by mapping one graph to the other.
- Connection tables are used to communicate the molecular graph to and from the computer, and the simplest type consists of atomic numbers and bond pairs.
- Linear notations like SMILES are more compact than connection tables and are useful for storing and transmitting large numbers of molecules.
- SMILES notation represents atoms by their atomic symbol and uses uppercase for aliphatic atoms and lowercase for aromatic atoms.
- Stereochemistry and geometrical isomerism are indicated in SMILES using specific symbols and notations.
- A canonical representation is a unique ordering of atoms for a given molecular graph, and the Morgan algorithm is a widely used method for this.
- The Morgan algorithm involves iterative calculation of connectivity values of atoms to enable differentiation and establish a unique order.
- The CANGEN algorithm has been developed to generate a unique SMILES string for each molecule.
Test your knowledge of structure searching and computer representations of chemical structures with this quiz. Explore methods such as canonical SMILES algorithm, substructure screening, molecular graph representations, and linear notations like SMILES.
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