MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'drug design'. Sat, 03 Sep 2011 02:51:52 +0100 http://www.medworm.com/index.php?rid=3546885&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2010%2F05%2Fmolecular-design-and-molecular-modeling.html After a recent question on Blue Obelisk Exchange and ChemPedia Lab about molecular drug design (see also cross-post) and a recent book about molecular modeling basics I thought it is time highlighting more information on that topic.Drug design principles, molecular modeling, and use in medicinal chemistry:C. Bissantz, B. Kuhn, and M. Stahl, A Medicinal Chemist’s Guide to Molecular Interactions, J. Med. Chem., 2010, Article ASAP. DOI 10.1021/jm100112jBioisosterism and bioisosteric design principle articles.J. H. Jensen, Molecular modeling basics, 2010.Summary slides about molecular modeling (quantum chemistry) of Noel O'Boyle: (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=3546885 Sat, 08 May 2010 19:21:00 +0100 3546885 http://www.medworm.com/index.php?rid=2796486&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F09%2Finnovation-20-looking-for-strategy-in.html "You can’t control what you can't measure." [Tom DeMarco]I am strongly believing in people-centric innovation for drug design and health care. Still, we have serious challenges to solve before this can happen, and a lot of them are in-vivo, not in-silico:Get rid of the negative group dynamics.Accept information overload and embrace collaboration.Bridge silos, e.g. chemical data silos, but also break-down legal or license hurdles, e.g. by using micropayments.Please find below the slides and handout for my talk in October on the BioIT World conference. The conference will cover a large range of life science topics, e.g. -omics, semantics, technology, bioinformatics, life science software, collaboration platform, etc. This is all very exciting and I am looking forward to those talks and mee... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2796486 Mon, 14 Sep 2009 18:21:00 +0100 2796486 http://www.medworm.com/index.php?rid=2463051&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F06%2Fgoogle-wave-drug-design-federation.html "The Google Wave Federation Protocol may succeed email (an innovation from 1965), as the dominant form of Internet communication."[Google Wave Federation Protocol @WP]Google launched Google Wave. It is a mind-blowing technical platform, which might just "change" publishing, health support of patients and physicians, and any other industry, where knowledge workers are suffering from keeping found things found (KFTF) and collaboration security (see conference blogging, libel law, compliant commenting, medicine 2.0 danger). I do not think the GWave will replace collaboration tools, but it might enrich them, by facilitating information moderation and bridging (for all peers and channels).You can check first the Google Wave presentation (almost 1.5 hours), or continue reading below.What is the ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2463051 Sun, 07 Jun 2009 17:02:00 +0100 2463051 http://www.medworm.com/index.php?rid=2441536&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F05%2Fwe-know-that-scientific-collaboration.html We know that scientific collaboration is important, but what is holding people back to contribute to web 2.0 communities (of people, like you!) ?This question was raised on FriendFeed (another web 2.0 platform, a good one). Though I answered parts of this question earlier, here a focus on the increasing number of compliance regulations, especially for people in industry (e.g. drug design). Beside, please check also the dangers in health/medicine 2.0.Science And Compliant CommentingView more OpenOffice presentations from Joerg kurt Wegner. (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2441536 Tue, 26 May 2009 20:18:00 +0100 2441536 http://www.medworm.com/index.php?rid=2389849&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F05%2Fdrug-design-and-thinking-unthinkable.html "The problem pharma industry faces isn’t that they didn’t see generics coming. They not only saw it miles off, they figured out early on that they needed a plan to deal with it. ... In drug design the unthinkable scenario unfolded something like this: The ability to share data and intellectual properties wouldn’t shrink, it would grow. Walled data silos would prove unpopular and inefficient. ... No one experiment is going to replace what we are now losing with designed drugs, but over time, the collection of new experiments that do work might give us the cure we need." [adapted from Clay Shirky]We need legal support, intellectual property protection, and social legal systems, we need them more than ever ! Sure, we want to work 'openly' together, but not without payment. I think ther... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2389849 Wed, 06 May 2009 18:32:00 +0100 2389849 http://www.medworm.com/index.php?rid=2312608&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F03%2Fopen-innovation-in-drug-design-i-do-not.html Triggered by slides and a discussion from Cameron Neylon was I wondering, to which degree people believe in open innovation for the drug design community?Though the principle seems valid for a few software companies, is there little support for life sciences on this topic."It's an area that's just not been explored much. The usual flow is very much linear. Can be developed in academia, is then licensed via tech transfer." [Deepak]"The question is whether a business can make money by a route that doesn't involve patents (or copyright). There are examples of that, O'Reilly publishing being the most obvious but they are pretty thin." [Cameron]In other words, if you do not need the money, do whatever you like openly. If you need the money, e.g. for clinical trials, then please make sure stayin... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2312608 Mon, 30 Mar 2009 17:30:00 +0100 2312608 http://www.medworm.com/index.php?rid=2510888&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F03%2Fdo-drug-innovation-while-information.html People thought always drug design is rational. Nowadays, things might have changed (maybe) ... and technology alone is not the solution. IT might support collaboration and information management, but we need seriously (a timely) action of legal advisors on supporting democratic-action and intellectual-property-protection.Nova Spivack has posted the interesting idea that the number of questions is faster growing than the number of answers. This forces us to ignore more facts, which leads us away from rational decision making, if we are not collaborating. I think, he has the point that in some areas we are facing bounded rationality in phases of a work process. On the other hand, I am willing to ignore information about the south of orion and rather read another drug design paper instead. Th... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2510888 Wed, 18 Mar 2009 20:27:00 +0100 2510888 http://www.medworm.com/index.php?rid=2286142&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F03%2Fdo-drug-innovation-while-information.html People thought always drug design is rational. Nowadays, things might have changed (maybe) ... and technology alone is not the solution. IT might support collaboration and information management, but we need seriously (a timely) action of legal advisors on supporting democratic-action and intellectual-property-protection.Nova Spivack has posted the interesting idea that the number of questions is faster growing than the number of answers. This forces us to ignore more facts, which leads us away from rational decision making, if we are not collaborating. I think, he has the point that in some areas we are facing bounded rationality in phases of a work process. On the other hand, I am willing to ignore information about the south of orion and rather read another drug design paper instead. Th... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2286142 Wed, 18 Mar 2009 20:27:00 +0100 2286142 http://www.medworm.com/index.php?rid=2249561&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F03%2Fdrug-design-paradigms-get-involved-in.html "The availability of pharmaceuticals must not be taken for granted. Pharmaceutical research requires expertise, a large commitment, a great deal of patience and the courage to take large financial risks. What counts is a sustainable framework in Germany (and other countries, too) as a location for the pharmaceutical industry. This is not a guarantee for economic success but is certainly at its foundation." [we get involved - vfa innovation]"To bring personalized medicine forward, scientists, regulators, policy makers, and pharmaceutical company leadership will need to find ways to more successfully work together, adopt a new mindset, and take a networked approach to innovation—one in which we can successfully share pre-competitive information and common platforms such as biomarkers, geno... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2249561 Sun, 08 Mar 2009 11:55:00 +0100 2249561 http://www.medworm.com/index.php?rid=2056475&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F12%2Fdrug-designers-are-creating-innovative.html "The FDA will approve at least 21 first-of-a-kind drugs this year, up from 18 in 2007. And the number of black-box warnings decreased by 25 percent. The boxed warnings are the most serious a drug can carry." [salon.com]It is well known that researchers in pharma are facing challenging times. Nonetheless, the FDA has approved increased the number of approved drugs last year (21 drugs compared to 18 in 2007). This in combination with the increasing innovation in pharmaceutical research gives hope for the next years.The question for me is, can this industry still be innovative with all those layoffs, and still make it a mission possible for the next years? I know that some people think that technology can help"The constant march of technology makes it possible for a smaller work force to do ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2056475 Sat, 20 Dec 2008 14:54:00 +0100 2056475 http://www.medworm.com/index.php?rid=2047962&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F12%2Fgroup-contribution-revisited-via.html "What chemists really need is reliable data, and biophysical techniques" [FBDD events 2009](via practical fragments)In the world of fragment-based ligand discovery, researchers hope that two fragments, when linked together, will behave at least additively: the free energies of binding for each fragment will sum together, with a multiplicative effect on affinity. In ideal cases, linked fragments will behave synergistically. But all too often, linking two fragments produces disruptive behavior, and the resulting molecule actually binds less tightly than would be predicted based on the binding energies of the individual fragments. This occurs not just when linking fragments, but in fragment merging and growing as well. Can such phenomena be modeled?The mathematical groundwork was described mo... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2047962 Wed, 17 Dec 2008 19:33:00 +0100 2047962 http://www.medworm.com/index.php?rid=1865683&cid=t_164078_149_f&fid=35780&url=http%3A%2F%2Fwalkerma.wordpress.com%2F2008%2F10%2F10%2Fseptember-10-2008%2F I came across an interesting site that provides useful information for anyone interested in computer aided drug design. BindingMoad.org is a database derived from the PDB, but includes only high resolution protein structures with bound ligands. Other information such as binding data is also included.        (Source: one in ten thousand) one in ten thousand blogs http://www.medworm.com/rss/comments.php?id=1865683 Fri, 10 Oct 2008 12:22:47 +0100 1865683 http://www.medworm.com/index.php?rid=1677469&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F08%2Fdata-models-or-both.html Correlation supersedes causation, and science can advance even without coherent models, unified theories, or really any mechanistic explanation at all. [C. Anderson, Wired, 2008-07-16]First, I disagree with this statement. Second, thanks to bioinfoman3@delicious for sharing this information.Honestly, I do not get it, why are people claiming that the scientific community, e.g. drug design, is similar to the chip industry or google concepts. Here, Chris Anderson claimed that data alone will replace theoretic concepts. As said by others, in the comments to his article, is data alone not information. Amund Tveit confirms this by showing that data correlations alone might be misleading, because you can find correlations in everything, even if it makes no sense. Data means any data, so if you lo... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1677469 Sun, 03 Aug 2008 18:01:00 +0100 1677469 http://www.medworm.com/index.php?rid=1658240&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F07%2Fquotes-from-neighbors-july-2008.html ==Receptors: Can't Live With 'Em, Can't Understand 'Em (In the pipeline)==At various points in my drug discovery career, I’ve worked on G-protein-coupled receptor (GPCR) targets. Most everyone in the drug industry has at some point – a significant fraction of the known drugs work through them, even though we have a heck of a time knowing what their structures are like.For those outside the field, GPCRs are a ubiquitous mode of signaling between the interior of a cell and what’s going on outside it, which accounts for the hundreds of different types of the things. ...==A-β Dimers- The Long-Sought Minimal Culprit in Alzheimer's Disease? (The Curious Wavefunction)==Following on the heels of the headline-making Nature publication that demonstrated that NSAIDs (Non-steroidal AntiInflamma... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1658240 Sun, 27 Jul 2008 19:27:00 +0100 1658240 http://www.medworm.com/index.php?rid=1423277&cid=t_164078_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F284391217%2F Here is the abstract of a paper in Hypertension entitled Structure-based identification of small-molecule angiotensin-converting enzyme 2 activators as novel antihypertensive agents. Angiotensin-converting enzyme 2 (ACE2) is a key renin-angiotensin system enzyme involved in balancing the adverse effects of angiotensin II on the cardiovascular system, and its overexpression by gene transfer is beneficial in cardiovascular disease. Therefore, our objectives were 2-fold: to identify compounds that enhance ACE2 activity using a novel conformation-based rational drug discovery strategy and to evaluate whether such compounds reverse hypertension-induced pathophysiologies. We used a unique virtual screening approach. In vitro assays revealed 2 compounds (a xanthenone and resorcinolnaphthalein) t... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1423277 Tue, 06 May 2008 05:40:13 +0100 1423277 http://www.medworm.com/index.php?rid=1238249&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F02%2Fsocial-search-in-drug-design-and-what.html Social search engines, another kind of social software, are trying to include user knowledge for improving search results in the future. One example is Wikia with an announcement of Jimmy WalesSearch is part of the fundamental infrastructure of the Internet. And we are making it open source. In contrast to the problem described by randfish might this improve search quality and reduce search engine tweaking requirements by users. Sometimes users have e.g. to multiply search terms or to find other tweaks, for getting the search results you want. Early initiatives like the the open directory project DMOZ (@Wikipedia) are using already user organized classification schemes for web links. SWiK organizes open source project information in a Wiki-like manner.I am still a little bit puzzled to und... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1238249 Sun, 17 Feb 2008 19:07:00 +0100 1238249 http://www.medworm.com/index.php?rid=1147418&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F01%2Fboutique-drugs-splitting-mass-market.html "Recently, the term boutique has started being applied to normally-mass-market items that are either niche or produced in intentionally small numbers at very high prices. For example, before the release of the Wii, a Time Magazine article suggested that Nintendo could become a boutique video-game company, producing games for niche audiences, rather than trying to compete directly with Microsoft and Sony [1]" [Boutique@WP]"articles intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease in man or other animals and articles (other than food) intended to affect the structure or any function of the body of man or other animals." [FDA definition]As found via Bio-IT/drug discovery expect analysts in the future more boutique drugs. Two main causes are mentioned.Fi... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147418 Sat, 05 Jan 2008 21:15:00 +0100 1147418 http://www.medworm.com/index.php?rid=1147419&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F12%2Fcommunity-moves-on-merry-xmas-and.html As posted by Deepak and Egon have several chem-/bio-informatics community members reached another milestone by publishing about userscripts in life sciences. In short, I am a believer in this technology. When reading, I got a little bit disappointed, because I got left with the feeling that I start loosing the touch to the community, though I try to follow and contribute as much as possible.Loosing grip became also clear when I read the posts of Ola and Egon. I know that the community needs a self-selecting oligarchy for moving forward. You guys meet regularly in workshops and user group meetings. Some people might not have the time for this. In other words, you are part of the hard-core development team. This means, if you are not explaining the problems in more details and post more info... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147419 Sat, 22 Dec 2007 18:30:00 +0100 1147419 http://www.medworm.com/index.php?rid=1100289&cid=t_164078_149_f&fid=35780&url=http%3A%2F%2Fwalkerma.wordpress.com%2F2007%2F12%2F17%2Fuseful-site%2F Free computer tools in Structural Bioinformatics and Chemoinformatics (Source: one in ten thousand) one in ten thousand blogs http://www.medworm.com/rss/comments.php?id=1100289 Mon, 17 Dec 2007 20:35:30 +0100 1100289 http://www.medworm.com/index.php?rid=1147423&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F11%2Fandy-grove-when-silicon-indoctrinates.html Andy Grove is right and we, the drug design community, can learn something from the chip industry. Derek, can you not see it, too? This strong relationship between those two families ..."If you want to understand why something happens in business, study the disk drive industry. Those companies are the closest things to fruit flies that the business world will ever see. Drug design is a process between 9 to 15 years! So, which object to study lies in-between a fruit fly and a hard-disk? A high-throughput screening, a biological assay or an 'in silico' 3D/2D/xD model of a drug?" [Mining Drug Space] (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147423 Wed, 07 Nov 2007 21:11:00 +0100 1147423 http://www.medworm.com/index.php?rid=1147424&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F11%2Fcommenting-on-grim-days-for-pharma.html via business|bytes|genes|moleculesBloomberg says that drug sales are forecast to grow at their slowest ever rate in 44 years. The WSJ reminds us that FDA approvals for NMEs are slow, and on a downward curve. Perhaps it’s time for the pharma industry to really think about Pharma FutorologySome of the consequences have been announced, and I think everybody hopes that those things will not happen every single year!Can innovation help us for making drug design a mission possible? If yes, what are potential key factors for success?Aligning scientists and goalsPutting scientists in the driver's seatGoal congruencePositive self-imageFair evaluation system for high-performing scientistIndustral cultures that foster innovationTake calculated risksOpenness and transparencyAdapt to constant changes... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147424 Sat, 03 Nov 2007 01:35:00 +0100 1147424 http://www.medworm.com/index.php?rid=1147426&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F11%2Fsix-rules-for-creating-data-driven-drug.html "The problem is that we live in the most perfect imperfect medium in the world: the Web.For now it is impossible to collect data perfectly. It is ugly, it is dirty, it is incomplete and no matter how hard you try it is not going to get perfect.Yet we can’t resist." [Occam's razor]Hahaha ... what a great statement of Avinash. Lets translate his statement about "Six Rules For Creating A Data Driven Boss!" into a drug design setting for getting "Six Rules For Creating a Data Driven Drug Design Project!".# 1: Get Over Yourself"In the past, many experimentalists shared a similar sentiment regarding of the usefulness of theoretical and computational methods to their drug discovery problems, namely: You're always explaining to me after the fact why a molecule i've already discovered is active, ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147426 Fri, 02 Nov 2007 18:14:00 +0100 1147426 http://www.medworm.com/index.php?rid=1147433&cid=t_164078_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fsix-sigma-in-drug-design-old-hands-or.html K. Ramakrishnan asked the question Will implementation of Six sigma, TQM, ISO improve efficiency or hinder the innovation?What would be an ideal process or methodology to improve innovation in drug discovery?What would be the best methodology or way to build an integrated team with good communication and coordination to accelerate both innovation and efficiency in drug discovery?Might there be a connection to the six degrees of drug design? And what helps more? Old hands or fresh blood? Are people here just playing with buzz-words or can anybody really give some more information about those topics? (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147433 Sat, 15 Sep 2007 21:54:00 +0100 1147433