Cheminformatics OLCC Topics 1
This follows David’s book.
Modules
Information Management (1-4 weeks, depending on school)
a. Introduction to the Chemical Information: Literature and Data
1. DOIs (Concept and unique identifier, role is being expanded to including data)
2. URIs/IRI
b. Document & Citation Management Systems
1. Mendeley
2. Zotero
3. EndNote
4. Refworks
5. BibTex
I.
II.
History and Introduction to Cheminformatics (1 week)
Representing 2D chemical structure on computer
a. Historical Ways of Representing Chemicals
b. SMILES line notation
c. InChI line notation
d. Graph theory and internal representation
e. File-based formats
f. Representing nuances
g. Representing reactions and generic structures
III. Characterizing 2D structures with descriptors and fingerprints.
a. Fragmental descriptors
b. Physicochemical properties
c. Topological indices
d. Assembling descriptors into fingerprints
e. Measuring similarity between fingerprints
IV. Storing and searching 2D structures in databases
a. Moving beyond simple files of chemicals
b. Database technologies
c. Structure, substructure and similarity searching
d. Representing substructure queries in SMARTS
e. Client-side interfaces to databases
f. Searching example using PostgreSQL and CHORD
g. Freely available searchable chemical datasets
V. Handling chemical reactions on computer
a. Chemical reactions
b. Reaction databases
VI.
VII.
VIII.
IX.
X.
XI.
XII.
Representing 3D chemical structures on computer
a. Where do 3D structures come from
b. Dealing with conformational flexibility
c. Representing 3D conformers on computer
d. Generating and manipulating 3D structures with a computer
e. 3D pharmacophores
f. 3D Descriptors and fingerprints
g. Databases of 3D structures
h. Available 3D databases
Chemical structures on the web and in the scholarly literature
a. Requirements for handling chemical information in documents
b. Making structures in documents machine readable
c. Contextualization
d. Accessibility
Cheminformatics in the chemistry library
a. Commercial tools and datasets covering the chemistry literature
b. Free cheminforamtics resources, datasets and tools for chemistry library
c. Emerging trends in the chemistry library
Analyzing chemical datasets using clustering and diversity
a. Cluster analysis
b. Hierarchical clustering
c. Nonhierarchical clustering
d. Diversity analysis
e. Coverage and cell-based methods
f. Relative diversity
g. Comparing datasets
h. Diverse subset selection
Predicting biological activities of chemical compounds
a. Quantitative Structure-Activity Relationships (QSAR)
b. Nonlinear approaches to QSAR
c. Virtual screening
d. Evaluating predictive modles
Working with 3D chemical structures
a. Visualization of 3D structures and proteins
b. Molecular Superposition
c. 3D QSAR
d. Molecular Docking
e. Molecular modeling tools
Programming toolkits for cheinformatics
a. Chemistry Development Kit (CDK)
b. OpenBabel
c.
d.
Chemistry Descriptors Library
Workflow tools