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some products... I pointed to one clear paradox here in the article, like pointing the readers to SPORCalc, I have no conflict of interest with this study or reference, it is just that it points to a very specific work, this I would say it is self promotion, it does not explain anything to readers nor give them an overview of what is available etc... To me you have a major paradox here, you say that click2drug or vls3d or some other related that users could add... is conflict of interest, or people who want to advertise their work etc... but please, between a directory of resources and one specific software, if i had to choose, obviously the directory of tools make sense as it points to basically all the work done (essentially again free tools and databases) by the scientific community in one area. Then too bad, these resources are maintained by human beings, like most resources and thus points to some names, what is the problem with this ? A computer can not generate such list accurately, thus some names show up, otherwise
Knowledge should remove all the references to scientific articles but here again they point to some names, and why this name and not that one... ? Clearly, I would rather see the papers of people who have some background written down here than people eventually totally out of the field and topic... So all of this is a mess, if one follows all recommendations nothing should be written at the end and indeed, this article does not move, it is stuck and i understand that if as soon as somebody add some knowledge the data are removed, then, this is done, no point to even have an article. It is interesting that editors seem to prefer old references that have no much meaning today that contributions that bring a bit of novelty and general knowledge.. This is to me a clear conflict of interest between the editors and the users the readers. If you ask a biologist if they want to see SPORCalc or a list of tools, i am sure they want a list of tools. But again, from my side i have nothing to win. I am just running a big lab, just running in a PhD school with 200 PhD students and 400 senior scientists working in all areas of life sciences and health sciences, so if you like the article the way it is, again, no problem. I ll stop here and let other users or else try to do something, they might succeed to move things, maybe maybe not... End of the story from my side Again, I have nothing to sell, nothing to win, no promotion and my Ego is not requiring attention, I do not care, I have a permanent position, etc... My impression, although i have many things to learn about Knowledge, is that some people play with it, you mentioned people
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relation with the Click2drugs group but I know their work, like most people in the field. When you say thank for coming to talk, I could return the question, why do you delete everything without discussing with the users or people ? This is surprising to me. Are you here to tell the rest of us what to think ? what could be useful for instance for biologists who are trying to work with rational design ... The way this article is written, people do not get much help with rational design, at least from the silico tools that are available today. Of course they read that a simulation some 10 years ago was helpful, but please, it does not really help a biologist here to know this. I added the VLS3D site because in my opinion it contains a lot of in silico tools that assist drug design, it is maintain by people working in the field, it is updated as compared to many other related sites that stopped implementing tools in 2011 or 2012.., there, nothing to sell, most of the tools a free to use, at least for academic people, students, and most of the time for the private sector as well. Thus, if you ask me some rational, what is the point to give users one package, SPORCalc, in the middle of nowhere, users should get a list of tools and not one tool, and decide what is good for them. The SPORCalc, published in 2009 has been cited in 17 studies, well, why is this tool here then ? Why one tool and not a list of tools ? Many references are old and of no interest in 2015. For many sections, some major reviews, well cited reviews... should be added. As it seems that we are on a page that benefits some private interests and some people and not the community, I ll not interfere, I just stop here. I do not fit, you decide until new editors will come and hopefully optimize the page
1192:"ligand based" design but they do exist (some older CNS drugs come to mind). Finally it is quite common to use several different design techniques on the same project. For example, pharmacophore based database searching (i.e., virtual screening) is often used to identify hits while structure based design techniques may be used to optimize the hits. There are now many drugs currently on the market in which computer-aided drug design (CADD) techniques contributed significantly. HIV protease inhibitors and carbonic anhydrase inhibitors immediately come to mind. The application of these techniques has become so wide spread that it is probably now the exception rather than the rule when a drug makes it market without at least some contribution from CADD. I will try to add more examples when I get a chance.
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section be added to outline what parts of the drug discovery process the drug design principles can be applied to (move the content from para. 4 of "Computer-aided drug design" to its own short section above "types" section) (c) the scoring material from the "computer-aided-design" should combined with the scoring material in "structure-based-method" (except the material for dock scoring methods), and either be put it their own "scoring methods" section or be added where appropriate to the existing structure.
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These ideas must be reduced to practice and that is the task of drug discovery. At the same time, I believe that the drug design article should not be merged into drug discovery since the former is already fairly long and merging it into the later would give undue weight to drug design. Furthermore the field of drug design is fairly well developed and the subject of many review articles. On that basis, drug design deserves its own article.
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for more about that. One of the challenges that experts face, is while they are very accomplished in their given field, when they first come to
Knowledge they don't understand the policies and guidelines governing content and sourcing in Knowledge (which can be confusing), and can get pretty prickly
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We collaborate with the doctor on matters related to patent litigation. Why do you keep insisting that any quote of his work, however relevant, is promotional? The tone adopted is always neutral and the content is verifiable and relevant to the issue under consideration. We do not promote anybody. We
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I have added various templates at the top of the article, that indicate clearly that this article badly needs attention. These were removed and I have replaced them. Such templates should not be removed until the problems have been addressed. The section on neural networks is badly written, contained
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This new article was created as one sentence and then proposed for speedy deletion. I removed the deletion tag and added context and more material. Nevertheless, we do not need this article. More details of the computer methods used in drug design should be added here and the article made a redirect.
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Redundancy 3: The introduction says "rational drug design" is another name for "drug design", yet there is a section in the article (section 3) on "rational drug discovery". Drug design is one approach to drug discovery, so the is no more-precise refinement offered by having a section on "rational
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I agree that drug design is a subset of drug discovery. Drug discovery comprises all the activities (chemical synthesis, biological assays, etc.) that are required to find a new drug. Drug design, in the way it is usually defined, is restricted to the development of ideas of what might be a drug.
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There is clearly an important point being discussed here and it seems to me that the pages mentioned above should be merged and perhaps some sections under these pages become new pages describing special cases. My feeling is that the over-arching topic is "drug discovery." I would suggest that "drug
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It would be wonderful to have some examples to illustrate each of the drug design approaches mentioned in the article. The way the article reads now makes it difficult to decipher whether the methods described are in common practice or are hopeful approaches. The "Structure based" section ends with
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parameter is "to provide a short explanation describing the issue". Third, I dispute that there was anything contradictory in the lead. The term drug design has both a narrow and a broad definition. It is important to include both definitions in the lead and there is nothing contradictory about
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I understand that rules are needed. I checked wikipedia introduction about what seems to be self promotion for instance for an external link, and it seems that a link that points to a web site written by authoritative experts in the field... are appropriate, if this site is not selling or related
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Sir, I do not have a conflict of interest with the doctor. I do not get compensated in any way by his organizations nor do I have any connection to him other than one informal exchange of opinions on a legal matter in 2011. I read the COI policy and cannot find any of what you are referring to. I
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Redundancy 2: "structure-based drug design". there appears to be redundancy and overlap of scope of the whole "structure-based" section 2.2 with the "Computer-aided drug design" section, I don't see a necessary distinction between these separate sections in the overall organizational scheme. It
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Drug design is largely restricted to the "hit to lead" and "lead optimization" stages of drug discovery. Even in these stages, there are a lot of activities such as chemical synthesis, in vitro and in vivo assays, crystallography or NMR, etc. that go on in parallel with drug design. Therefore I
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citing narrow literature more than a decade old, the lede makes narrow, academic, and contradictory statements that are editor- rather than expert- and industry opinion, initially limiting discussion to RDD, then wandering, ultimately focusing on the more traditional "ligand design" perspective,
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i do not understand your statement, I am, and the people at Click2drugs, a scientist working in the field for about 30 years. Just asking with this tone gives the idea that is page is maintained by some fascist party. As you ask like if i was or they were criminals, here is the answer: I have no
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Suggested improvements: (a) I think the introduction should contain a link to the Drug
Discovery page, and general discussion of drug discovery can be removed from this page (e.g., the "rational drug discovery" section), drawing some content into other sections if it must be kept. (b) A short
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I agree that nebulous phrases such as "these techniques are raising much excitement to the drug design community" should be replaced with concrete examples. It appears that most of the examples listed in the "examples" section used "structure based" design methods. There are fewer examples of
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I have been trying to add a link also very relevant to the topic, WWW.VLS3D.com and just like for the clik2drugs link, i have been removed by Jytdog. I do not understand the rational, how such an article with old and obsolete references can not be updated by experts in the field ! Interesting
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The material on scoring functions is included as a subsection of structure based design hence these are not in separate sections. Furthermore scoring function ≠structure based design. Rather scoring functions are used for structure based design. Hence I do not see this main section and it's
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is the product of rational design - as far as I know it comes out of a high-throughput screen as described in
Deininger's and Druker's paper introducing Imatinib to the clinic and two chemical papers on Imatinib Would anyone be opposed to me removing this paragraph from the examples section?
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The present article on drug design is not up to date, many of the references are of no help... But it looks some people do not want any change, I looked at the history and definitively, this is strange... So continue this way and nobody will even read it anymore... If this is the goal fine
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Recent edits have been made by an obvious new editor with few wiki-markup skills. I am assuming good faith and hope that someone can continue to clean these up. They do however give far too much undue weight to neural networks software. I brought back a paragraph that talked about molecular
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quote: "The COI guideline does not absolutely prohibit people with a connection to a subject from editing articles on that subject. Editors who have such a connection can still comply with the COI guideline by discussing proposed article changes first, or by making uncontroversial edits."
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That being said, neural nets do have legitimate applications in drug design. However these applications are supplementary and are far from the only way to perform drug design. Therefore I suggest this material may be appropriate for a separate article, but only if is it backed up by
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These sections take the extreme viewpoint that " cannot be used to discover a totally new drug molecule ... with the help of computer" with abundant evidence to the contrary (see citations in the current version). Therefore these sections are in clear violation of
Knowledge's
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not every "molecular modification" is of drugs but that article talks only about drugs, it has a very very vague title name! it could apply to the petrolchemical industry aor to biology. I think this article should have a main, further or for tag linking to that and vice versa
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Redundancy 1: Scoring methods. Scoring methods are discussed in paragraph 3 of section "Rational Drug
Discovery" and again in paragraph 2 of section "Computer-aided drug design". A separate set of docking scoring methods are discussed in section "Scoring Method" (section
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seems to me that all structure-based drug design requires computer-aided methods (e.g., ligand-fragment linking "requires a large amount of computation"), and separating out the computer-aided methods makes the article feel redundant by the time you reach reading about it.
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an advert that is inappropriate and it is difficult to follow. It also implies that this is the only approach to drug design, which is incorrect. It gives overdue weight to neural networks and it is written in a way that is quite inappropriate for an encyclopedia. --
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After further checking, it turns out that the "master" formula that was presented was not Böhm's. I have added Böhm's formula and will try to track down the source of this "master" formula. Once I get this all sorted out, I will probably move much of the detail to
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Hi - for background, you might or might not be surprised to hear that a lot of people try to use
Knowledge to advertise their products and services; academics also try to use Knowledge to promote their own work. Both are an abuse of Knowledge, per the policy
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Neural networks play at most a minor role in drug discovery as currently practiced in the pharmaceutical industry and for that matter, as studied in academia. So as mentioned above, more than a passing mention of neural nets in an article this length gives
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and is also fairly generic. This was the first scoring function published and variants of it are still widely used by others. What is needed is mention of some of the other methods (e.g., empirical- and knowledge-based) for balance. I will work on this.
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The description of a structure based selectivity filter was added today and later removed by Jytdog, indicating that it is self promotion. The work is relevant to structure-based drug design. I don't understand why that is self promotion.
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rather than discussing, is typical of folks who edit with a conflict of interest. It was a simple question about clik2drugs, you answered it, and that is done. I didn't ask about VLS3D.com - are you related to the folks who run that
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I think this is a semantic issue. Rational/drug design can be defined in a variety of ways. Rational design in the broadest sense is design knowing the target, and hence screening for tyrosine kinase inhibitors
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I tagged the article for repetition, because structure-based drug discovery and scoring methods are described separately in separate section. The organization on the whole could be improved.
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Traxler P, Bold G, Buchdunger E, Caravatti G, Furet P, Manley P, O'Reilly T, Wood J, Zimmermann J (Nov 2001). "Tyrosine kinase inhibitors: from rational design to clinical trials".
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There are numerous claims such as " the ... latest technique being applied to discover new drugs" without a single citation to backup these claims in clear violation of
Knowledge's
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Yes, I agree that this article has major problems. Adding redundant, condescending, and inaccurate comments especially about lead are not helpful. Focus on improving the article.
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Did not mean to suggest that scoring methods and structure-based drug discovery were redundant with each other. Rather, each topic is mentioned multiple times through the article.
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OK, we are all on the same page - drug design is really cool and interesting, and i don't think our article does it justice..... do you think the tags are excessive now boghog?
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doing so. Finally I agree that the article needs a lot more work. The errors of omission can easily be fixed and no one has claimed that this article is complete (see
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Please do keep in mind that this is an encyclopedia and is meant to describe things - not tell people how to do things nor provide them tools for doing things -- see
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It is clear that there is a lot more to drug discovery than drug design. To illustrate, the pharmaceutical R&D pipeline can be roughly be divided as follows:
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The stability of the protein is sacrificed in order to create a binding site and this loss of stability may be "recaptured" by binding an appropriate ligand
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when their edits fail to "stick" because their edits don't comply. I will be happy to work with you to help you learn about them. Good luck, in any case!
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the sentence: "These techniques are raising much excitement to the drug design community" and the citation of some rather old reference material.
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Capdeville R, Buchdunger E, Zimmermann J, Matter A (Jul 2002). "Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug".
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Clearly the sourcing needs to be improved. But adding tags to the entire article, to sections, and to individual citations is excessive.
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which was marked as a primary source, this is a classic paper that according to Google
Scholar has been cited 933 times. I have added
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I'm brand new to
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thank you for coming to talk, finally. one thing at a time. what is your relationship with the folks who run clik2drugs? Thanks.
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Is there even one example of a drug that has been developed using "structure based design" - or are there any in clinical trials?
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which is a very recent review article that cites the classic paper. I think it is appropriate that both citations are retained.
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think the drug design and drug discovery articles need to be kept separate. On the other hand, I would support merging of the
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to have drug properpties and "design" approaches simply limit the field of candidate chemicals based on available knowledge.
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OK, you absolutely have a conflict of interest with regard to Ariel Fernandez. I will continue this on your Talk page.
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There are a number of problems with this statement. First and foremost, it violates a fundamental Knowledge policy,
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communication here ! If people get some insights about drug design with is here, fine with me.. no time to waste
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Three successful examples of drug design at Novartis using a tyrosine kinase as a molecular target are described.
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Would it be possible to reconsider this link, and eventually let it in this page in the section "external link"?
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ignoring ... contemporary integrative small molecule design concepts, e.g., that include physical property and
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Deininger MW, Druker BJ (Sep 2003). "Specific targeted therapy of chronic myelogenous leukemia with imatinib".
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quote Ariel Fernandez when he has done something relevant to the matter discussed, plain and simply.
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This merge proposal was made in May, but there has been no discussion here. I support the merge. --
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on Knowledge. If you would like to participate, please visit the project page, where you can join
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on Knowledge. If you would like to participate, please visit the project page, where you can join
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This article was the subject of a Wiki Education Foundation-supported course assignment, between
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Koehler KF, Rao SN, Snyder JP (1996). "Modeling Drug–Receptor Interactions". In Cohen NC (ed.).
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It is not my area yet I am 100% certain they need to merge. Interstingly, this is not the only
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for those articles and some of the cross-linked articles mentioned, too. For example mentiones
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I am completely removing the sections dealing with neural networks for the following reasons:
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it gives a list of software and web servers dedicated to drug Design from several providers.
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Thanks for comments from Boghog2 here and above in the discussion of "discovery vs design".
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ignoring contemporary integrative drug design concepts that include physical property and
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if there are tags on sentences in sections, i agree that is too much. one or the other!
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mechanics, ab initio, DFT etc. There is however still undue weight to neural networks. --
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Buchdunger E, Zimmermann J, Mett H, Meyer T, MĂĽller M, Regenass U, Lydon NB (Mar 1995).
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Buchdunger E, Zimmermann J, Mett H, Meyer T, MĂĽller M, Druker BJ, Lydon NB (Jan 1996).
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I have tracked down the source (or at least one source) of the master equation to
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Please clarify, what is your relationship to Ariel Fernandez or his lab? Thanks.
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it is a serious page handled by people from the Swiss institute of Bioinformatics,
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drug discovery". It's like having a section titled "Blue" in the "Blue" page.
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Drive-by comment that the recent edits are a big improvement; nice work
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it is clear you have a conflict of interest. In addition, there is an
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is probably UNDUE for one approach and is not what we want in WP per
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All that said, I agree that the article very much needs updating; we
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From a review article co-authored by E. Buchdunger and J. Zimmermann:
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that makes sense - I hear you on the generality of the formula.
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design" is a bit of a misnomer, since in practice chemicals are
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However, the link seems to have been removed (automatically?).
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I am confused since one of the first sentences there contains
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in the banner shell. Please resolve this conflict if possible.
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This article has been given a rating which conflicts with the
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it's not an advertising or a link to a commercial web site,
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Wiki Education assignment: Adv Molecular Bio Bass-FSU-Fa23
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Hi Jytdog. Perhaps some of the details could be moved to
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Looking at the examples provided, I would not agree that
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I tried to add the following external link to this page:
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Side note: I would say that drug design does more than "
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hi boghog in my view the specific equation presented in
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every one of your edits promotes Ariel Fernandez. See
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So is rational drug design the same as drug design? --
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This is covered in the second paragraph of the lead.
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228:A record of the entry may be seen at
7:
1947:. The behavior you demonstrated of
536:I think this link makes sense here:
403:This article is within the scope of
311:This article is within the scope of
2173:focus on the edits, not the editors
1830:This article needs serious addition
1028:article where you cannot really do
270:It is of interest to the following
23:for discussing improvements to the
2360:
2356:
556:Thank you for your help, Vincent
445:project-independent quality rating
331:Knowledge:WikiProject Pharmacology
14:
2434:Mid-importance Chemistry articles
2419:WikiProject Pharmacology articles
822:lead optimization (+ drug design)
334:Template:WikiProject Pharmacology
236:
2363:. Further details are available
2350:
1443:Druker BJ, Lydon NB (Jan 2000).
396:
372:
304:
283:
252:
188:
45:Click here to start a new topic.
2404:Knowledge Did you know articles
662:, which sounds very similar to
510:) 09:14, August 20, 2007 (UTC).
457:This article has been rated as
423:Knowledge:WikiProject Chemistry
351:This article has been rated as
2439:WikiProject Chemistry articles
1492:Nature Reviews. Drug Discovery
1275:18:52, 24 September 2013 (UTC)
1238:14:59, 24 September 2013 (UTC)
1016:02:38, 23 September 2007 (UTC)
977:02:29, 23 September 2007 (UTC)
426:Template:WikiProject Chemistry
1:
2409:B-Class pharmacology articles
2389:03:46, 16 November 2023 (UTC)
2379:— Assignment last updated by
2299:Scoring functions for docking
2253:Scoring functions for docking
2230:Drug_design#Scoring_functions
1585:12:04, 14 November 2013 (UTC)
1552:04:40, 14 November 2013 (UTC)
1536:23:59, 13 November 2013 (UTC)
1004:Computer-assisted drug design
813:hit finding/target validation
417:and see a list of open tasks.
325:and see a list of open tasks.
42:Put new text under old text.
2148:that included the following
1824:06:24, 22 October 2014 (UTC)
1726:01:58, 22 October 2014 (UTC)
1699:01:35, 22 October 2014 (UTC)
1682:01:11, 22 October 2014 (UTC)
1653:00:49, 22 October 2014 (UTC)
1639:00:47, 22 October 2014 (UTC)
1619:23:54, 21 October 2014 (UTC)
1026:computer-dependant Process X
691:23:42, 7 February 2007 (UTC)
646:22:35, 7 February 2007 (UTC)
633:21:21, 7 February 2007 (UTC)
593:07:06, 7 February 2007 (UTC)
1216:13:09, 14 August 2009 (UTC)
1202:18:46, 13 August 2009 (UTC)
1184:14:24, 13 August 2009 (UTC)
950:18:32, 13 August 2009 (UTC)
710:13:56, 13 August 2009 (UTC)
50:New to Knowledge? Welcome!
2455:
2429:C-Class Chemistry articles
1969:who edit according to the
1144:18:33, 28 April 2009 (UTC)
1094:22:12, 22 April 2009 (UTC)
1073:09:08, 14 April 2009 (UTC)
927:Drug discovery hit to lead
664:Drug Discovery Hit to Lead
652:discovered and/or designed
463:project's importance scale
357:project's importance scale
2336:15:09, 22 June 2015 (UTC)
2311:13:57, 22 June 2015 (UTC)
2292:12:44, 21 June 2015 (UTC)
2278:11:52, 21 June 2015 (UTC)
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1542:subsection as redundant.
684:drug development pipeline
680:development of a new drug
488:somewhere, presumably at
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80:Be welcoming to newcomers
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1906:03:46, 13 May 2015 (UTC)
1889:21:06, 12 May 2015 (UTC)
1856:21:13, 12 May 2015 (UTC)
932:Pre-clinical development
860:Investigational New Drug
855:pre-clinical development
678:that some goals are the
676:pre-clinical development
577:07:47, 7 June 2010 (UTC)
314:WikiProject Pharmacology
219:impedes many efforts at
199:appeared on Knowledge's
2236:.... thoughts on that?
1971:policies and guidelines
1294:Pharmacological Reviews
1046:19:21, 8 May 2008 (UTC)
996:19:28, 8 May 2008 (UTC)
598:I think the historical
1743:Dehydron PubMed search
1377:10.1073/pnas.92.7.2558
1257:
966:molecular modification
612:rational choice theory
260:This article is rated
241:
75:avoid personal attacks
2367:. Student editor(s):
1115:neutral point of view
637:But wouldn't that be
498:comment was added by
406:WikiProject Chemistry
337:pharmacology articles
239:
100:Neutral point of view
1263:reverse pharmacology
1163:Any one out there?
1034:mathematical biology
1032:without a computer,
882:New Drug Application
660:Screening and Design
602:part is assigned to
105:No original research
2049:-Tox concerns early
620:bounded rationality
2365:on the course page
1792:Unknown parameter
1522:Tag for Repetition
616:rational ignorance
429:Chemistry articles
266:content assessment
242:
217:chemical synthesis
86:dispute resolution
47:
2182:WP:WORKINPROGRESS
2127:10.1021/ci500731a
2025:Excessive tagging
2021:
2004:comment added by
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1919:comment added by
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1813:
1778:External link in
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1838:— Preceding
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1800:suggested) (
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1708:— Preceding
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1208:Johnfravolda
1172:Johnfravolda
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1134:. Cheers.
1089:(Discussion)
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