From Visualization Sp06
- Schematic Drawings of Protein Structures. Richardson. (pdf)
- History of Molecular Visualization. Martz and Francoeur. (html)
- Computer-Generated Pictures of Proteins. Lesk and Hardman. (pdf)
- Describing Patterns of Protein Tertiary Structure. Richardson (pdf)
- Anatomy and Taxonomy of Protein Structure. Richardson. (html)
- Molecule of the Month. Goodsell. (html)
There are many programs out there for visualizing molecules. If you are curious, here are a few to explore:
Jschonbrun - Apr 19, 2006 10:40:06 am
I realize that "Schematic Drawings of Protein Structures" assumes you are quite familar with protein structure. I encourage you at least skim it though, because it is one of the few attempts to articulate the princples of molecular visualization. And many of Richardson's ideas may apply generally to conveying shape.
I've been looking for some web pages that provide a visual introduction to protein structure, but haven't found too many good ones. Here are a few to take a look at, both for content and form:
Bryan - Apr 27, 2006 09:43:44 am
I very much enjoyed this lecture. I thought the problem was interesting most of all because while molecules are visual objects, we don't have any photographs of them to use as a starting point for designing visualizations. It was interesting to compare the "state of the art" diagrams with alpha helices, etc. to a more "physically" representative ball-and-stick or space-filling model. This visualization problem is a great example of what the viewer needs to see drastically affecting the representation.
Jschonbrun - May 01, 2006 04:41:18 pm
I didn't talk about this as much as I perhaps should've in my lecture, but I think Molecular Visualization can be a great framework for testing the efficacy of different visualizations for different needs. As you point out, the best representation depends on what the viewer is trying to see.
In particular, I'm interested in the Protein Folding Problem. This is essentially an optimization problem: finding the best molecular configuration according to an energy function. Despite a ton of research, search algorithms for this optimization problem are still not very successful. This largely of because of complex relationships between the many degrees of freedom.
I've been interested for some time in whether or not human guided search can help with this problem. This provides a very concrete metric of visualization effectiveness: which visual representations help humans find more optimal folds?
Yi-Tao - May 02, 2006 08:53:44 am
What was really interesting was how many simplified visualizations existed to represent complex proteins. During lecture, the topic of coloring molecules came up. The readings also talk about Functional Color Code and density coloring but nothing about coloring based on backbones or patterns. Has there been any work in that area?
Jschonbrun - May 02, 2006 01:08:14 pm
I'm not sure exactly what you by backbone color or pattern coloring. There are visualizations where certain types of secondary structure are assigned colors. (e.g. Helices = purple, Strands = gold.) And there is the "rainbow" coloring of the backbone. There are some other color schemes in Rasmol, such as "shapely", where each of the 20 amino acid types is assigned a color. And these colors are selected such that amino acids with similar types have similar colors.
Actually, the optimal way to color the 20 amino acids presents an interesting visualization mini-problem. The optimal system would allow for a viewer to visually distinguish each amino acid if concentrating on it. But perhaps also group amino acids with similar properties to give an overal impression of the organization of a structure. I believe the Shapley color scheme was designed to do this, though I could not find an accounting of how it was derived. [rgb values here]. It might be interesting to start with a pure qualitative, or labeling, scheme from ColorBrewer, and then try to extend it such that similar amino acids have similar colors.
Mattkam - May 02, 2006 05:24:17 pm
I wasn't able to attend this lecture due to the CHI conference. But the discussion thread made me recall my difficulties understanding molecular and cell biology, and how static representations in textbooks are sometimes inadequate. It would be cool to have computer-generated visualizations that we can interact and learn from.
Out of curiosity, I did a search on Google and found that there is some interest in this area at the intersection of molecular visualization and education, e.g. the Workshop on Molecular Visualization in Science Education (http://pro3.chem.pitt.edu/workshop/), the International Conference on Science Education and Visualization (http://www.grc.uri.edu/programs/2001/sciedu.htm), Molecular Visualization for Undergraduate Bioscience Teaching (http://www.umass.edu/microbio/rasmol/ws_short.htm), etc.
Have there been any learning assessments conducted to see if computer-based molecular visualizations are an improvement over textbooks?