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- Representation of Chemical Structures
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3. Chemical file formats and line notations
- Prof. Achim Zielesny
- Visualization of Chemical Structure
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4. Common types of visualization of chemical structure
- Prof. Robert M. Hanson
- Basic Algorithms in Cheminformatics
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5. Ring searching and aromaticity detection
- Prof. Dr. Christoph Steinbeck
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6. Substructure searching, similarity calculations and fingerprints
- Mr. Mark Rijnbeek
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7. Canonization, Morgan algorithm, equivalence classes
- Dr. Markus Meringer
- Structure Databases
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8. Storing, searching and dissemination of chemical information
- Prof. Achim Zielesny
-
9. Databases, indices and structure-related queries
- Dr. Wolf-Dietrich Ihlenfeldt
- Quantitative Structure-Activity/Property Relationships
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10. Overview of descriptors
- Dr. Jörg Kurt Wegner
- Machine Learning in Cheminformatics
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11. Introduction to machine learning and its application in chemistry
- Dr. Nikolas Fechner
- Cheminformatics in Drug Discovery
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12. Virtual screening
- Dr. John H. Van Drie
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13. Pharmacophore methods in drug discovery
- Dr. John H. Van Drie
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14. Pragmatic virtual fragment-based ligand design
- Dr. Marcus Gastreich
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15. Chemogenomics
- Dr. John P. Overington
- Molecular Modelling
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16. Molecular modelling: empirical methods
- Prof. Tim Clark
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17. Molecular modelling: electronic structure methods
- Prof. Tim Clark
- Computer-Assisted Structure Elucidation
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18. Methods for NMR-spectrum prediction
- Dr. Wolfgang Robien
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19. Cyber-based structure elucidation
- Prof. Morton E. Munk
- The Chemical Semantic Web
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20. Semantic chemistry: an overview
- Dr. Nico Adams
- Open Notebook Science and the Open Access Movement in Chemistry
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21. Open research: motivation, theory, and practice
- Dr. Cameron Neylon
- Archived Lectures *These may not cover the latest advances in the field
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22. Representation of chemical structures
- Dr. Thomas Engel
Printable Handouts
Navigable Slide Index
- Introduction
- Chemical structures in the computer
- Hierarchy levels of molecular representation
- Representation of chemical structures
- Nomenclature/notations
- Systematic (IUPAC) nomenclature and structure diagrams
- Chemical notations
- Excursion: the Königsberg bridge problem (Graph theory) (1)
- Excursion: the Königsberg bridge problem (Graph theory) (2)
- Application of Graph theory in chemistry
- Mathematical definitions in Graph theory (1)
- Mathematical definitions in Graph theory (2)
- Selection of matrix representations of graphs
- Coding the constitution: adjacency matrix (1)
- Coding the constitution: adjacency matrix (2)
- Incidence matrix
- Distance matrix
- Bond matrix
- Bond-electron matrix (1)
- Bond-electron matrix (2)
- Connection table
- Redundant connection table
- Non-redundant connection table
- Issues in structure representation
- Markush structures
Topics Covered
- Chemical structures
- Molecular representation
- Nomenclature and notations
- structure diagrams
- Chemical notations
- Matrix representations
- Markush structures
Talk Citation
Engel, T. (2024, October 31). Basics in cheminformatics: representation of chemical structures 1 [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved November 14, 2024, from https://doi.org/10.69645/GQHH6691.Export Citation (RIS)
Publication History
Financial Disclosures
- There are no commercial/financial matters to disclose.
Basics in cheminformatics: representation of chemical structures 1
Published on October 31, 2024
37 min
A selection of talks on Biochemistry
Transcript
Please wait while the transcript is being prepared...
0:00
Hello. A very warm welcome to
this introductory course on
The basics in Cheminformatics.
My name is Thomas Engel from
the University of Munich
and I will give you
an overview of
representation methods
of chemical structures
in the next slides.
0:22
Now let's start
with a big picture
representing chemical
structures in a computer.
One of the major tasks in
cheminformatics is to
properly represent
chemical structures in
an unambitious and unique
manner considering
the constitutional and also
the stereochemistry
of molecules.
The latter is very important
for storing molecules.
For example, in
databases but also
for structure and
substructure search.
But how could this be done?
Mostly the first step is to draw
a chemical structure by using
such a structure
editing software which
first of all, makes a picture of
a chemical compound that
carries much information for
the chemists but not
for the computer.
In order to process
the chemical structure on the
computer, we have to teach
the computer chemistry
and transform
the molecular structure into
a language amenable to
computer representations.
Basically, computers can only
handle bits of one in zero.
Coding is the basis for
transferring the data
into other forms of
representations, for example,
such a 3D viewing program
but also other
applications for example,
for synergies planning or
chemical reaction prediction.
But also the other way
around generate molecules
or structures for example
from measured spectral data.
But as each coding may
not include all pieces
of information.
For example, 3D information
or stereochemistry
may have interpretable
coding rules.
The transformation is
not always exhaustive,
unambitious, or even unique
as we will see in the
following slides.