Talk:Docking (molecular)

Click2Drug.org

Dear all,

I tried to add the following external link to this page:

• Click2Drug - Directory of computational drug design tools.

I think this link makes sense here:

• it's not an advertising or a link to a commercial web site,
• it is a serious page handled by people from the Swiss institute of Bioinformatics,
• it gives a list of software and web servers dedicated to drug Design from several providers, including docking software and web servers, as well as tools to prepare virtual HTS runs.

However, the link seems to have been removed (automatically?).

Would it be possible to reconsider this link, and eventually let it in this page in the section "external link"?

Thank you for your help, Vincent —Preceding unsigned comment added by Vzoete (talk • contribs) 08:01, 7 June 2010 (UTC)

I agree that the Click2Drug link is not spam. This link is hosted by a non-commerical side and is in turn is a comprehensive list of links to non-commerical and commerical third party docking software. In my opinion, this list of links is very well done and is very appropriate to this article. Linking to this site greatly reduces the need to include other external links in this article as for example was subsequently added in a new "Docking web servers" section. At the same time, I have reverted the "Docking web servers" links added in this edit. This are for the most part redundant to links contained in the Click2Drug link and in addition were added as a section outside the external links section which is not according to the WP:MOS. Boghog (talk) 09:38, 7 June 2010 (UTC)

Some of the concepts that should be added to this entry

• Consensus scoring
• Incremental construction (as in FlexX)
• de novo design
• filtering (such as in Glide)

--Dockingman 19:17, 30 April 2006 (UTC)

Removed penicillin comment

The use of penicillins will soon be obsolete as bacteria continue to evolve beta-lactamases that confer resistance to nearly every penicillin derivative that has been found to be active. Most betalactamases are susceptible to inhibition by clavulanic acid, and the metallobetalactamases, which are not, are rare. Changes to PBP targets causes serious resistance (eg in MRSA) which is not mediated by betalactamses at all. --ben 09:52, 25 June 2006 (UTC)

External links?

The list on external links is very much a commercial listing... should it be trimmed/modified?

• I agree that this list is inappropriate, therefore I have deleted this section. Boghog2 23:15, 20 October 2007 (UTC)

Rewrite

I found this article very confusing since it stated that the purpose of docking is to predict whether a molecule will bind. However this is not correct. The purpose of docking is to determine (1) the best relative orientation between two molecules in a complex and (2) the conformation of each molecule in the complex. Given this orientation, it is then the job of the scoring function to determine whether the interaction between these two molecules will be favorable. Therefore I have done a major rewrite of several of the sections to make this distinction clearer. Boghog2 23:25, 20 October 2007 (UTC)

Free energy

The free energy link points to a disambiguation page. I assume this should link to the "Free energy perturbation" page, but I'm not sure. I suggest to have the link pointing to the right page, not a disambiguation page. Hedgehawk (talk) 22:08, 15 September 2008 (UTC)

Thanks for your note. Per your suggestion, I have changed the link from Free energy to Gibbs free energy. Cheers. Boghog2 (talk) 22:16, 15 September 2008 (UTC)

Thanks for the correction. I learn something every day ;) Hedgehawk (talk) 22:22, 15 September 2008 (UTC)

Article to be merged?

Here is an article that goes into some detail on protein-ligand docking: searching the conformational space for docking. The article's name is clearly not a good one - but I don't know whether it should be renamed, or merged with this article instead. (If kept, it also needs to be sourced and wikified.) What do people think? Lfh (talk) 19:15, 10 May 2010 (UTC)

I think the searching the conformational space for docking article should be merged into this one after extensive copyediting, condensing, and sourcing. Boghog (talk) 20:16, 10 May 2010 (UTC)

OK. I've tidied it up a bit, and later I'll have a go at shortening it slightly. But I don't have the knowledge to source it, and the original author left the project years ago.

There is also some overlap between Docking (molecular) and Macromolecular docking. Lfh (talk) 11:35, 11 May 2010 (UTC)

Thanks for cleaning up the searching the conformational space for docking article. I have added a coupled of citations and trimmed it back further. Concerning Docking (molecular) and Macromolecular docking, the two topics certainly overlap, but I think there are enough differences in the approaches and goals that each subject deserves its own article. Boghog (talk) 20:27, 11 May 2010 (UTC)

MQQDAHRVSTPVEADSDTDNASIYADTLDNASYTTSVTSSVLDYQYENGRRYHSYHEGEYVLPNDEQEQDRLDLSHHIYLMLLKGELFQAPINNPKRVLDLGTGTGLWAIEYAEYVFFPPKISIKSTPNKQSSTNPNSQVIGIDLSAIQPSWVPPNCRFEIDDFEQPWSYSKPFDYIHGRELEGSIRDHDRLFKQALDNLNPNGWFEISSFDVNTYSDDGTHLGATNLLLSIKHMHESSRMFGKDTTSSPSWKDRMKKAGFVNVKEDVLKLPQSPWPKDPKLKELGRYHQLNMLEAMPIYTYVLFSRVLGWTRAEIEGLLAGIRMELRDTSYRLYTKVRVVYGQKPGGPVSA — Preceding unsigned comment added by 106.88.180.95 (talk) 01:37, 5 April 2015 (UTC)

List of software to a new page

I feel that it is reasonable to move/copy the list of protein-ligand docking software list to a new page of its own, similar to other lists of structure determination. Available at List of protein-ligand docking software. Vivek Rai (talk) 12:39, 11 January 2016 (UTC)

External links modified

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• Added archive https://web.archive.org/web/20160304232627/http://www.certara.com/products/molmod/sybyl-x/sbd/ to http://www.certara.com/products/molmod/sybyl-x/sbd/
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