New Thoughts on Chemical Visualization and Molecular Modeling
I’ve been asked to give a guest lecture at a computer science colleague’s graduate class on scientific visualization in February. She’s asking for a quick summary to put into her syllabus.
Her key question is this: what are problems that we are trying to solve in chemical visualization? What is the current state of visualization tools, and what would we dream of doing with them? It’s that last part which is the most interesting to me — what might we want to do if we had some ultimate tool?
Naturally I have some ideas of my own, but I’m interested in hearing some feedback. (I’ll post my ideas tomorrow.) How would you like to visualize molecules or chemical data sets? What features would you like to see in current visualization tools if you didn’t have to write the code?
Remember… the sky’s the limit!
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Pingback by Chemistry, “Tool Building,” and Brunelleschi’s Dome » geoff hutchison: blog — 2 years ago.
[...] Recently, I commented on problems and opportunities in chemical visualization. What features might we want to see in computer tools for molecular modeling? What do we need to have intuitive vision and easily build our chemistry? [...]
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Pingback by Visualizing Molecular Structure / Property Correlations » geoff hutchison: blog — 2 years ago.
[...] Recently, I wrote to ask for suggestions in chemistry visualizations. Rajarshi Guha wrote in with several suggestions. One of the most interesting to me was to map results or numeric data to structures themselves: In terms of mol vis itself, I’d like to see useful ways of mapping things to structures themselves – so fragment properties could be mapped to specific parts of a molecule, effects of descriptors in a QSAR model could be mapped to parts of a molecule and so on. Some of this has been done before, but is usually quite restricted. [...]
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Rajarshi Guha — 2 years, 2 months ago.
The first thing that comes to mind is visualizing high-D datasets associated with structures. But that’s not necessarily chemistry specific.
What I’d like to see are efficient ways to map numeric data back to structures. So rather than just do the usual procedures like MDS etc, can we represent the information in the numeric data in terms of relationships between structure and data (and not just low-D representations of the data).
Ok this is probably too vague! An example is an application at http://cheminfo.informatics.indiana.edu/~rguha/code/java/salivis/ which represents SAR information in the form of networks.
In terms of mol vis itself, I’d like to see useful ways of mapping things to structures themselves – so fragment properties could be mapped to specific parts of a molecule, effects of descriptors in a QSAR model could be mapped to parts of a molecule and so on. Some of this has been done before, but is usually quite restricted.
I suppose one blue-sky thing I’d like to see is a virtual reality style exploration of arbitrary chemical spaces – conceptually, not too difficult, especially since chemical spaces have been discussed before (cf ChemGPS by Oprea), but an efficient and intuitive tool would be great.
Also, you might want to take a look at Ben Shneiderman of U Maryland – he has some extremely cool and state of the art visualization techniques for large, high-D datasets
Noel O'Boyle — 2 years, 2 months ago.
See also Agrafiotis’s paper on SAR visualisation and software he has implemented at J&J.
Geoff — 2 years, 1 month ago.
Agrafiotis has two interesting papers: Advanced Biological and Chemical Discovery (ABCD): Centralizing Discovery Knowledge in an Inherently Decentralized World and SAR maps: a new SAR visualization technique for medicinal chemists.