Talk:Structural alignment

Hello WtMitchel. Let me introduce myself, i'm CEMS2 . I am one of the original author's of the Rosetta Structure prediction program. I have a long set of publications on the field of how to compare protein structures. And in How to use protein structure comparisons for many purposes. It's this last point which is subtle. There are an infinity of different structure overlap algorithms and the last thing the planet needs is yet another. And the reason we keep getting more and more of these is because people are not stopping to ask-- why do you want that structure overap anyhow?

It's the most important question. Is is local structure for function, is it evolutionary? Are you comparing mutations of the same protien? Are you looking for remote homologs? and you trying to figure out which resides should be paired in a new Blossum alignment matrix. When you ask that question a few algorithms stand out from the crowd. Many are not here, but mammoth that I am adding was really the very first one, that actually asked that question.

contemporary in time (2002) to SSAP (1998) and before TM. Notably Mammoth and DALI were the primary method structures have been compared at CASP.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479680/ It is one of four methods offered by the PDB (RCSB now) for the structural alignment tools.

so this is one of the grand daddy algorithms. 

it's key niches: What if you are comparing decoy structures from stucture prediction to real protieins? what about remote homologs where most superposition algorithms fail? Mammoth was the first algorithm to recognize that what you care most about is the E_value not the actual 3D overlap. How likely is this overlap by chance? SO it adds a lot to the discussion.

Below is a section in development.

• 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!

1. Some approaches use quaternerions to reduce the dimensionality of the space -- Actually, quaternions increase the dimensionality of rotation space.
2. 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)

I think you should be brave and fix this page!

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)

Cool! --Dan 15:34, 1 Apr 2004 (UTC)

Did a complete rework, hope it is a bit clearer... One could expand on the algorithmic side of things, as well as on the use of the method. Will try, as soon as I find time. Dr. Strangelove 20:00, 19 Jul 2004 (UTC)

---

The following comments made by me, Andrew Dalke <dalke@dalkescientific.com> on the Biopython mailing list. I don't like learning a bajillion wiki formatting conventions so I'm leaving this as-is on the talk page.

If it's two conformations of the same structure and the goal is to minimize overall RMSD through a single global alignment matrix then the usual reference I know is Kabsch

 [Kabsch, 1976] Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta. Crystal, 32A:922-923.
 [Kabsch, 1978] Kabsch, W. (1978). A discussion of the solution for the best rotation to related two sets of vectors. Acta. Crystal, 34A:827-828.

(The first had an ambiguity that could cause a sign error; fixed in the second.)

Several structure program implement that including:

 O - http://xray.bmc.uu.se/usf/factory_4.html
 VMD - http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node183.html
 PyMol - http://www.pymolwiki.org/index.php/Kabsch

This algorithm is not mentioned on the Wiki page and is 11 years older than the oldest mentioned reference. It isn't NP-hard as alluded to in the Wiki, since it's solving a much simpler problem.

The date for ProFit is strange on the Wiki. I knew about ProFit before the claimed 1996. The web site says http://www.bioinf.org.uk/software/profit/faq.html

No paper has been published describing ProFit itself since it is simply a convenient program (I hope) to let you use a standard fitting algorithm consequently, it is a little difficult to reference. The exact wording is up to you and dependent on the context, but I suggest something similar to:

Fitting was performed using the McLachlan algorithm (McLachlan, A.D., 1982 ``Rapid Comparison of Protein Structres, Acta Cryst A38, 871-873) as implemented in the program ProFit (Martin, A.C.R., http://www.bioinf.org.uk/software/profit/).

The McLachlan algorithm is also not mentioned in the Wiki.

I found a usenet announcement about ProFit at http://groups.google.com/group/bionet.software/msg/f219c5163bbadbdc?dmode=source&hl=en

 From: mar...@bsm.bioc.ucl.ac.uk (Andrew Martin)
 Subject: ANNOUNCE: Protein Fitting Software
 Date: 1995/07/20
 Message-ID: <1995Jul20.101545.37119@ucl.ac.uk>#1/1
 X-Deja-AN: 106640715
 organization: University College London
 newsgroups: bionet.software
 
 I've finally (after about 2 years) got around to fixing the last (?)
 remaining bugs in my ProFit protein least-squares fitting software and
 decided to make it generally available.

so the date should be 1995 or 1993 or earlier. I suspect the 1996 date came from the "first written" date for the documentation, at http://www.bioinf.org.uk/software/profit/doc/

what happened to the image? Str-alignment.png

according to the log the link was removed because the image was deleted from wikimedia

any way to link it back?

the list of available programs is gone.... think it was a good idea. —Preceding unsigned comment added by 146.203.21.23 (talk • contribs) 12:16, 3 July 2006

It was moved to Sequence alignment software, currently linked in the See Also section. It'll get a more prominent link when the list is in better shape. If you have any new additions, or a perspective on which packages are the most commonly used, that would be great! Opabinia regalis 00:11, 4 July 2006 (UTC)

'Sequence alignment software' perhaps is not the most accurate place for structure based alignment programs.—Preceding unsigned comment added by 146.203.21.237 (talk • contribs) 14:46, 7 July 2006

Structural alignment software now redirects there. I think the advantages of having everything in one place outweigh the minor disadvantage of following a redirect, but I'll put the question on the sequence alignment peer review if anyone else wants to chime in. Opabinia regalis 01:15, 8 July 2006 (UTC)

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)

Thanks for your image and useful copyedits. I added the relevant ref and clarified your examples to "computationally expensive" and "memory-intensive" respectively; I hadn't thought about that usage being confusing. Opabinia regalis 15:54, 30 September 2006 (UTC)

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)

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)

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)

I am concerned that this article no longer meets the good article criteria due to numerous uncited statements, including entire paragraphs. Is anyone willing to address this concern, or should it be sent to WP:GAR? Z1720 (talk) 00:53, 18 November 2024 (UTC)