Talk:List of protein structure prediction software

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Untitled edit

Latest comment: 15 years ago1 comment1 person in discussion

Rosetta@home does not really belong on this list. It cannot be used by researchers to predict structures. It is used to predict structures for the David Baker lab only. —Preceding unsigned comment added by 129.67.118.74 (talk) 13:11, 8 January 2009 (UTC)Reply

Availabilty? edit

Latest comment: 13 years ago1 comment1 person in discussion

It would be nice if a list like this included more information about availability. For instance, I would like to predict trans membrane proteins, but the mentioned programs are typically behind a web page that imposes limits on its use, and/or requires obscure licensing, often "available" by sending an email to some address which doesn't respond at all. Sorry about the frustration, but I've wasted a lot of time on academic software that clearly get orphaned as soon as the author gets his publication - it would be nice if there was some indication here or elsewhere on which programs are for real. Ketil (talk) 10:52, 1 September 2010 (UTC)Reply

TODO edit

Latest comment: 9 years ago1 comment1 person in discussion

This is what --Hsp90 (talk) 09:14, 27 October 2014 (UTC) found non-redundant from main article. Fit it to tables or delete.Reply

Princeton_TIGRESS (server) is a protein structure refinement server^[1] whose underlying method was ranked in 5th place in blind predictions during CASP10 (http://predictioncenter.org/casp10/doc/presentations/ranking_CASP10_refinement_DJ.pdf). It uses monte carlo and molecular dynamics based sampling techniques and support vector machines for selection. It can consistently increase the model accuracy of many top 3-D structure prediction servers' predictions, increasing the potential usability of a predicted structure in a biological application.

The Foldit program seeks to investigate the pattern-recognition and puzzle-solving abilities inherent to the human mind in order to create more successful computer protein structure prediction software.

The CAMEO Continuous Automated Model EvaluatiOn Server evaluates automated protein structure prediction servers on a weekly basis using blind predictions for newly release protein structures. CAMEO publishes the results on its website ([1]).

References

^ Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. "Princeton_TIGRESS: ProTeIn Geometry REfinement using Simulations and Support vector machines". Proteins. doi:10.1002/prot.24459.{{cite journal}}: CS1 maint: multiple names: authors list (link)

External links modified edit

Latest comment: 8 years ago1 comment1 person in discussion

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Latest comment: 6 years ago1 comment1 person in discussion

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Removing external links template edit

Latest comment: 6 years ago1 comment1 person in discussion

I would like to remove the external links template warning at the top of the page. This article is a "list" and it is my expectation that each entry has at least one direct link, and could also have footnotes, therefore it makes sense to have many links and the warning does not apply. I will go ahead and remove the warning if there are no objections? — Preceding unsigned comment added by LucasIglesias (talk • contribs) 17:11, 21 June 2017 (UTC)Reply

Adding info about IntFOLD? edit

Hi, I'd like to add the following regarding our IntFOLD server:

IntFOLD is an integrated server for modelling protein structures and functions from amino acid sequences.^[1] Each major version of the IntFOLD server has been independently tested in the CASP9-CASP12 experiments and its component algorithms have performed well, ranking among the top servers in the tertiary structure, quality assessment, disorder and function prediction categories (http://predictioncenter.org/). Over the years, the IntFOLD server has performed particularly well at self-estimates of 3D model accuracy. In the CASP12 experiment, according to the assessors formula the server ranked 3rd/5th (average Z-score > 0.0/–2.0) on the server only targets in the template based modelling category, and the McGuffin group manual target predictions ranked 1st/2nd (average Z-score > −2.0/0.0)^[2]^[3]. The tertiary structure predictions from the server are also continuously benchmarked on CAMEO (http://www.cameo3d.org). The method is competitive and continual performance improvements have been observed in the successive versions.

References

^ McGuffin, Liam J.; Atkins, Jennifer D.; Salehe, Bajuna R.; Shuid, Ahmad N.; Roche, Daniel B. (1 July 2015). "IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1". Nucleic Acids Research. pp. W169–W173. doi:10.1093/nar/gkv236.
^ Kryshtafovych, Andriy; Monastyrskyy, Bohdan; Fidelis, Krzysztof; Moult, John; Schwede, Torsten; Tramontano, Anna. [10.1002/prot.25425 "Evaluation of the template-based modeling in CASP12"]. Proteins: Structure, Function, and Bioinformatics. pp. n/a–n/a. doi:10.1002/prot.25425. {{cite web}}: Check |url= value (help)
^ McGuffin, Liam J.; Shuid, Ahmad N.; Kempster, Robert; Maghrabi, Ali H.A.; Nealon, John O.; Salehe, Bajuna R.; Atkins, Jennifer D.; Roche, Daniel B. [10.1002/prot.25360 "Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods"]. Proteins: Structure, Function, and Bioinformatics. pp. n/a–n/a. doi:10.1002/prot.25360. {{cite web}}: Check |url= value (help)

New Section/Table on Quality Assessment methods? edit

Latest comment: 6 years ago1 comment1 person in discussion

Do you think this page needs a new section/table on Model Quality Estimation/Assessment methods? — Preceding unsigned comment added by LiamMcGuffin (talk • contribs) 11:46, 14 December 2017 (UTC)Reply

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AlphaFold edit

Latest comment: 2 years ago1 comment1 person in discussion

Why is AlphaFold not included in the list of protein structure prediction software? Jarble (talk) 01:10, 30 July 2021 (UTC)Reply

Add topic

[khoury2013-1] Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. "Princeton_TIGRESS: ProTeIn Geometry REfinement using Simulations and Support vector machines". Proteins. doi:10.1002/prot.24459.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[2] McGuffin, Liam J.; Atkins, Jennifer D.; Salehe, Bajuna R.; Shuid, Ahmad N.; Roche, Daniel B. (1 July 2015). "IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1". Nucleic Acids Research. pp. W169–W173. doi:10.1093/nar/gkv236.

[3] Kryshtafovych, Andriy; Monastyrskyy, Bohdan; Fidelis, Krzysztof; Moult, John; Schwede, Torsten; Tramontano, Anna. [10.1002/prot.25425 "Evaluation of the template-based modeling in CASP12"]. Proteins: Structure, Function, and Bioinformatics. pp. n/a–n/a. doi:10.1002/prot.25425. {{cite web}}: Check |url= value (help)

[4] McGuffin, Liam J.; Shuid, Ahmad N.; Kempster, Robert; Maghrabi, Ali H.A.; Nealon, John O.; Salehe, Bajuna R.; Atkins, Jennifer D.; Roche, Daniel B. [10.1002/prot.25360 "Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods"]. Proteins: Structure, Function, and Bioinformatics. pp. n/a–n/a. doi:10.1002/prot.25360. {{cite web}}: Check |url= value (help)

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