Talk:Structural alignment software

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Untitled

This page really needs to be revised. Some links are broken; often there are only links to the server, although a download is available.

Flexible?

What is meant by the column flexible? It should be specified in the table description. -- 140.142.20.229 (talk) 22:04, 10 December 2010 (UTC)[reply]

I have added a description of this column (see article page) - it indicates methods that allow structures to "bend" around "hinges" or some other technique to treat protein structures as other than rigid bodies. Alexs2008 (talk) 00:01, 2 May 2011 (UTC)[reply]

Does 'nil' indicate that the method does not support flexible alignments, or that no one has yet input that information? We should change it to either 'No' or blank. --Quantum 7 20:11, 22 March 2013 (UTC)[reply]

A number of the algorithms that are listed as 'flexible' here actually have no adaptation to changes in molecular conformation beyond simple range thresholds. --MinotaarContributor (talk) 05:58, 29 December 2013 (UTC)[reply]

Topology independence

Another common property of alignment algorithms is whether they support topology-independent (sometimes called sequence-order independent) alignments or not. Would this information be useful to add to the table? It seems like good information, but the table's already getting a bit wide for my screen.

I've started a table at User:Quantum7/Structure alignment software to start to keep track of the new column. If anyone would like to contribute please do. --Quantum 7 20:24, 22 March 2013 (UTC)[reply]

Alternating table row colors

The alternating row colors do improve legibility, but have two major faults

When inserting or reordering rows, the colors of all following rows must be modified.
Sorting the table leads to random row colors

I asked about bot-based solutions to #1 at Wikipedia:Bot requests/Archive 54#Updating tables with alternating rows. I think that solving #2 would require modifying the sorting javascript. Of course, the easiest solution would be to remove row colors entirely. For a preview of this, see User:Quantum7/Structural alignment software. Personally, I like the alternating row colors and think they improve readability. Suggestions? --Quantum 7 21:48, 22 March 2013 (UTC)[reply]

References

Currently only the first author and date for the publication of the method are given. These are nice for sorting, but perhaps a full reference for published algorithms would be useful? It's sometimes hard to find original citations for methods on their servers. --Quantum 7 22:03, 22 March 2013 (UTC)[reply]