Cheminformatics Topics

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Robert Belford
Robert Belford's picture
Cheminformatics Topics

List and discussion of various tools associated with Cheminformatics.  The objective is to identify topics that should be covered, and then create a forum for each of those. The topics of the additional forums can eventual evolve into lessons and TLOs.


From David: the following are topics that I have taught previously, but I don't want to assume these are necessarily relevant for the undergraduate level. That would be best determined by people who work more closely with chemistry undergrads:

Representation of 2D structures on computer
Characterizing 2D structures with descriptors and fingerprints
2D chemical database searching systems
Reaction representation and databases
Representation and characterization of 3D chemical structures
Chemical structures on the web and in the scholarly literature
Cluster and Diversity analysis
Quantitative Structure-Activity Relationships (QSAR) and Predictive Models
3D visualization, alignment, docking and scoring
Optimization Algorithms in cheminformatics
Data mining of chemical & biological information
Tools for cheminformatics algorithm development
Here are some other topics we might consider, with potential people who might be interested
Using freely-available chemistry structure databases (ChemSpider, PubChem, ...) [Tony Williams, Evan Bolton]
Cheminformatics journals [David Wild, David Martinsen, ...]
Online cheminformatics resources
A big question is to whether organization should be functional (as above) or chemistry use-case driven


Abhik Seal
Abhik Seal's picture
Using Cheminformatics Tools for Assignment

The idea I would suggest is to develop videos and manuals for using open source tools for small assignments in cheminformatics .

Milind Khadilkar
Milind Khadilkar's picture
About cheminformatics scope and topics

The topics do look good.I had some occasions a few years ago to introduce cheminformatics to practicing chemists (production/QC/R&D) and graduating and post graduate Chemistry/Pharma students, as also to Informatics and Math professionals. It was a difficult task because I have had little formal training in chemistry.(I generally tried to cover the following (only as highlights) in 2 sessions of 90 minutes each, and failed on every occasion:  Computer Representation of Chemical Structure, Molecular Fingerprints, Similarity, Substructure and Identity search, Linear Notation (SMILES); The concept of InChI, Canonicalization; molecular libraries. Cheminformatics Tools and resources)What I am putting below is from recollection of those days in 2005-6 when InChI was new on the horizon. I am out of touch on these things and so these might no longer be relevant.------ By representation do we mean all of the following (from among others)? (a)abstract mathematical representation(b)representation as appropriate data structures/data objects (with associated algorithms) in a programming language(c) representation as data/structures/data objects in a running computer program(d) visual static and dynamic 2D and 3D representations(renderings)(e) in-memory representations in terms of calculated positions, lengths and angles(f) representation of data (including photographs/spectra etc.) collected through various kinds of equipment/storage chambers etc.(g) representation for the web using CML(h) storage to and , search and retrieval from databases(i) SMILES, InChI etc,  Do we also include representation of other moieties and objects generated through thought processes like retrosynthesis?Must we include "biological" information processing in this?Don't we include "Applications of Cheminformatics" which are somewhat out of ordinary, like inventory control and Markush structures in patenting, for example?Cheminformatics probably means different things to different people. Are we focussing on "Structure and Reaction" cheminformatics rather than on informatics related to thermodynamics, interfacing of computers and lab equipment, integration of data from different sources etc.?</li> I am unfamiliar with the American education system and hence have no idea what the chemistry (and informatics) curriculum for the target student group of Cheminformatics OLCC is. Some of the "representations" listed above will be difficult without the students having exposure to some "good" programming language.About the organization: I would prefer chemistry use case based. ideally, instead of being a separate course, cheminformatics content can be woven within chemistry courses. But yes, that could be difficult too.Thanks.

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