Talk:Structural alignment

message: * Structural alignment is vague; needs more info; should be more specifically named (perhaps Protein structural alignment --Stewart Adcock) +sj+ 09:52, 2004 Feb 22 (UTC)
This entry is not only bad, but probably full of mistakes. Plese feel free to voice your opinion, create new topics where appropriate and generally change at will the contents of this page.
The correct refence to cite SARF2:
Alexandrov, N.N. SARFing the PDB. Protein Engineering (1996), 9:727-732. 
There is a mistake in the authorship of SARF2 program.
:You aren't wrong about it being full of mistakes!
:#Some approaches use quaternerions to reduce the dimensionality of the space -- Actually, quaternions increase the dimensionality of rotation space.
:#The Dali algorithm (named after Salvador Dali) uses network isomorphism between the contact networks of two proteins to perform alignment. -- DALI is an abbreviation of Distance matrix Alignment.
: Stewart Adcock 23:21, 20 Feb 2004 (UTC)
replies: text: Don't worry, I definitely will -- when I have time.  I even have a report that I could wikify. Stewart Adcock 17:15, 16 Mar 2004 (UTC)
replies: text: Cool! --Dan 15:34, 1 Apr 2004 (UTC)
thread_title:  From PNA/Biology

message: :1. Well written? Pass, upon changes below.
:2. Factually accurate? Pass
:3. Broad in coverage? Pass
:4. Neutral point of view? Pass
:5. Article stability? Pass
:6. Images? Pass
:6. Appropriate referencing? Pass, upon changes below.
Additional comments: Some changes needed.
*However, at O(n10 / ε6) for a globular protein of n residues, the algorithm is still too expensive for practical use.
:::I don't think the algorithm itself is expensive, don't you mean expensive to implement in terms of CPU time?
*Representation of structures
:::No references in this section, could add one to cover the statement about improving data by discarding noise.
*This representation is expensive because the features in the square matrix are symmetrical...
:::Again, expensive isn't what you mean. TimVickers 14:06, 30 September 2006 (UTC)
thread_title: GA review

message: In the Methods section, only DALI, SSAP and CE should be included (but not TM-Align). DALI, SSAP and CE are considered "classical methods" in this area, and the papers on them have received a large number of citations (100+ for each). We should not describe the new and not-so-popular-yet methods like TM-Align, because there also exist several other structural alignment methods. (Please see http://en.wikipedia.org/wiki/Structural_alignment_software). If we include TM-Align, we also should include all of these methods. 
However, I would like to recommend to add some popular methods like: VAST (recognized by PDB), FATCAT (recognized by PDB), and SSM (recognized by SCOP).
:Thanks, for some reason this article fills up with good-natured but promotional text if unwatched. I've shortened the TM-align section (it was rather wordy and diffuse anyway) out of desire not to give new and 'exciting' methods undue weight; however, as a Zhang/Skolnick project I think it's notable enough to merit a blurb. The new arrangement also provides an easy way to add other new developments without bloating the article. 
:On the other methods, feel free to add sections on them if you're interested. VAST in particular, as it's quite old and maybe not used so much anymore, but a notable piece of the development of these techniques. Opabinia regalis 01:46, 20 December 2006 (UTC)
thread_title:  Pls remove TM-Align 

message: I would like to add a section explaining how the optimal alignment for a pair of molecules is computed using SVD.--Plediii (talk) 21:03, 1 February 2009 (UTC)
replies: text:  Apparently what I was looking for is subtly linked at the end of the introduction.  I'm trying to wrap my head around why these are separate articles. --Plediii (talk) 15:06, 2 February 2009 (UTC)
thread_title:  Why not explain the algorithm?