Jinboxu

RaptorX for protein structure modeling

RaptorX is a new protein structure prediction program developed by Xu group, excelling at the alignment of distantly-related proteins with sparse sequence profile and that of a single target to multiple templates. In particular, RaptorX can generate much better alignments than our previous single-template threading program RAPTOR. For example, RaptorX generated the best alignments for the 50 hardest TBM (template-based modeling) targets in CASP9 (the 9th Critical Assessment of Structure Prediction). RaptorX consists of four major modules: single-template threading, alignment quality assessment, multiple-template threading and fragment-free approach to free modeling. Due to limited computational power, the RaptorX server currently offers the first three modules for regular usage. The standalone RaptorX package is also available for download at the server page.

References:

Jian Peng and Jinbo Xu. RaptorX: exploit structure information for protein alignment by statistical inference. PROTEINS, 2011.

Jian Peng and Jinbo Xu. A multiple-template approach to protein threading. PROTEINS, 2011.

Jian Peng and Jinbo Xu. Boosting protein threading accuracy. In the Proceedings of the 13th International Conference on Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science. Vol. 5541, pp. 31-45, 2009. Springer.

Jian Peng and Jinbo Xu. Low-homology protein threading. Bioinformatics (Proceedings of ISMB 2010), 2010.

Speedy deletion nomination of RaptorX for protein structure modeling and alignment

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A tag has been placed on RaptorX for protein structure modeling and alignment, requesting that it be speedily deleted from Wikipedia. This has been done under the criteria for speedy deletion, because the article seems to be unambiguous advertising that only promotes a company, product, group, service or person and would need to be fundamentally rewritten in order to become an encyclopedia article. Please read the general criteria for speedy deletion, particularly item G11, as well as the guidelines on spam.

If you can indicate why the subject of this article is not blatant advertising, . Clicking that button will take you to the talk page where you will find a pre-formatted place for you to explain why you believe the page should not be deleted. You can also visit the article's talk page directly to give your reasons, but be aware that once tagged for speedy deletion, if the article meets the criterion, it may be deleted without delay. You may freely add information to the article that would confirm the subject's notability under Wikipedia guidelines. Please do not remove the speedy deletion tag yourself, but don't hesitate to add information to the article that would help make it encyclopedic, as well as adding any citations from independent reliable sources to ensure that the article will be verifiable. Feel free to leave a note on my talk page if you have any questions about this. SilverCityChristmasIsland 21:18, 22 August 2011 (UTC)

August 2011

Please do not add inappropriate external links to Wikipedia, as you did to RAPTOR (software) with this edit. Wikipedia is not a collection of links, nor should it be used for advertising or promotion. Inappropriate links include (but are not limited to) links to personal web sites, links to web sites with which you are affiliated, and links that attract visitors to a web site or promote a product. See the external links guideline and spam guideline for further explanations. Because Wikipedia uses the nofollow attribute value, its external links are disregarded by most search engines. If you feel the link should be added to the article, please discuss it on the article's talk page rather than re-adding it. Thank you. 4twenty42o (talk) 21:28, 22 August 2011 (UTC)

Hello Jinboxu. If you are affiliated with some of the people, places or things you have written about in the article RAPTOR (software), you may have a conflict of interest or close connection to the subject.

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Please familiarize yourself with relevant content policies and guidelines, especially those pertaining to neutral point of view, verifiability of information, and autobiographies.

For information on how to contribute to Wikipedia when you have a conflict of interest, please see our frequently asked questions for organizations. Thank you. SilverCityChristmasIsland 21:29, 22 August 2011 (UTC)

Please stop adding inappropriate external links to Wikipedia, as you did to Protein structure prediction with this edit. It is considered spamming and Wikipedia is not a vehicle for advertising or promotion. Because Wikipedia uses nofollow tags, additions of links to Wikipedia will not alter search engine rankings. If you continue spamming, you may be blocked from editing Wikipedia. Thank you. 4twenty42o (talk) 21:34, 22 August 2011 (UTC)

This is your last warning. The next time you insert a spam link, as you did at Protein structure prediction, you may be blocked from editing without further notice. Persistent spammers may have their websites blacklisted, preventing anyone from linking to them from all Wikimedia sites as well as potentially being penalized by search engines. SilverCityChristmasIsland 21:43, 22 August 2011 (UTC)

March 2013

Hello, I'm Shadowjams. I wanted to let you know that I removed an external link you added to the page Structural alignment, because to me it seemed inappropriate for an encyclopedia. If you think I made a mistake, or if you have any questions, you can leave me a message on my talk page, or take a look at our guidelines about links. Thanks, Shadowjams (talk) 13:56, 28 March 2013 (UTC)