What is the main goal of Docking@home ?
Message boards : Docking@Home Science : What is the main goal of Docking@home ?
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Does Docking@home mainly search for how proteins can lock onto (dock) with other proteins, viruses and bacteria to see how a particular protein can neutralise or aid some other protein/molecule to help fight diseases?
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Does Docking@home mainly search for how proteins can lock onto (dock) with other proteins, viruses and bacteria to see how a particular protein can neutralise or aid some other protein/molecule to help fight diseases? Hello, my name is Dr. Roger S. Armen PhD, and I am the primary scientist directing the development and application of molecular docking techniques for the Docking@Home project. I am a NIH funded postdoctoral fellow in the Charlie Brooks III lab at The Scripps Research Institute in San Diego. My research focuses on the docking of small molecules to proteins using computational chemistry. Although it is true that proteins indeed dock to other proteins, this is not the primary focus of our project for the first few years. Our project will focus on the docking of small molecules (drug- like molecules also called "ligands") to proteins and developing and extending our current methodology for protein-ligand docking. Protein-ligand docking is now a very useful step in the identification of new small molecules that may bind to a protein. A protein-ligand docking simulation can help direct experimental investigations of important proteins of interest, such as proteins implicated in diseases. In principle, protein-ligand docking may aid in the identification of new "drug-like" small molecules that may be re-designed into molecules with more favorable "drug-like" properties. Therefore, protein-ligand docking is a general computational method that may be useful in the "structure-based-design" of new drug-like molecules, or as a tool for the design of protein-ligand interactions in general. The immediate scientific goals of our docking@home project are aimed at the development of our protein-ligand docking methodology. Our CHARMM based docking method has already been established as one of the most accurate docking methods that currently exist for docking of a flexible ligand to a rigid protein. We intend to continue to develop, extend, and validate our methods on new and more difficult test cases. We intend to develop accurate methods to include protein flexibility in protein-ligand docking, which is currently one of the most pressing issues in the field of docking. The validation of such an approach on a wide variety of protein targets would be a very important contribution to the scientific community. I received a postdoctoral fellowship from the NIH for my proposal to solve this important problem in computational biology. Our secondary scientific goal is to apply our protein-ligand docking methods to important scientific problems. Eventually, we would like to open our site to collaborations with publicly funded experimental scientists who have a specific need for accurate protein-ligand docking, but do not have the time, resources, expertise or personnel for such a project. Thank you very much for your interest in the project. Dr. Roger S. Armen PhD |
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Thanks for explanation, very appreaciated.
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Is Docking@home a splitted project of predictor? |
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>>> I would like to thank you Dr Armen for your detailed response to my query. Your goals seem very worthwhile and I will enjoy crunching some data for you and your team and helping to sort out the problems of getting you the information that you require. |
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Michela
Forum moderator Project administrator Project developer Project tester Project scientist 
Joined: Sep 13 06 Posts: 163 ID: 10 Credit: 97,083 RAC: 0 |
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Is Docking@home a splitted project of predictor? Hi, there is a very useful link in the web page of predictor@home on this. Please look at: http://predictor.scripps.edu/scientific_update_cp.php under "Developing new application areas for P@H" Michela |
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Thanks for explanation, very appreaciated. With regards to our immediate scientific goal, our results will be used to improve our protein-ligand docking methodology and to validate our models. Developing and validating our methods will improve the effectiveness of our application of protein-ligand docking to real-world scientific problems and future collaborations with experimentalists. As a policy, I would prefer to not summarize what is done on other life-science BOINC projects, and I would direct you all to look at the pages explaining the science of each individual project for specific details. However, because we are a new site, I will provide a brief comparison of the general types of work that is done on each site. Rosetta@Home, Folding@Home, Tanpaku, and Predictor@Home all perform predictions about protein structure and protein folding. Rosetta@Home also performs predictions for protein design and protein-protein interactions. Dr. David Baker does an excellent job of explaining the potential applications of protein folding, protein design and protein-protein interactions to fighting disease here: http://boinc.bakerlab.org/rosetta/rah_medical_relevance.php SIMAP@Home uses sequence information to determine protein similarities and protein domains. The prediction of domains is also used for the functional annotation of proteins. FightAIDS@Home performs protein-ligand docking predictions using AutoDock. Their site specifically targets important HIV virus proteins. They are currently investigating the structural basis for the evolution of drug resistance in important HIV drug targets, with the goal of identifying new drug-like small molecules that are less susceptible to drug resistance. Our site Docking@Home will also perform protein-ligand docking predictions, but we are using a CHARMM based approach to docking, not AutoDock. Our immediate scientific goals are to improve and validate our docking methodology, and then to apply it to specific scientific problems. In the initial stages of our site, we will work on a large "test set" of protein-ligand complexes that includes important protein drug targets for HIV/AIDS, cancer and other diseases. During the initial stages of our project we intend to use these examples because they are of high interest to the biomedical community, well-studied, and have lots of excellent experimental data that we can compare to and validate our methods. I urge all of you to participate in as many of the life-science BOINC projects as possible as they each provide an important and unique contribution to the rapidly progressing field of computational biology. Thank You, Dr. Roger S. Armen PhD |
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>>> I would like to thank you Dr Armen for your detailed response to my query. Your goals seem very worthwhile and I will enjoy crunching some data for you and your team and helping to sort out the problems of getting you the information that you require. Thanks Conan, I will do my best to continue to provide detailed responses to questions as soon as possible. Thanks for participating in our project we really apreciate it. ____________ |
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Would the scientific results be free for the public ?
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Michela
Forum moderator Project administrator Project developer Project tester Project scientist
Joined: Sep 13 06 Posts: 163 ID: 10 Credit: 97,083 RAC: 0 |
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Would the scientific results be free for the public ? Hi, we plan to build a portal that shows the best results. We will keep the people posted on our achievements. We will use our result for research purposes and present them to the scientific community. Michela |
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Thanks for the answers, it is more obvious what Docking project is doing in term of science.
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Would the scientific results be free for the public ? Yes, scientific results will be freely availible for the public. Initially, we will most likely be the main user of our results, because we wish to test various models of protein flexibility for protein-ligand docking. So we will try a model and then see if it works to correctly predict known experimental results in difficult test cases where the protein is known to be flexible. Some models will perform better than others, and we will decide which results are likely to be "the most usefull" to other researchers in this area and then release them. Others researchers in this area can benifit from the release of our results. HIV protease is an excellent example of one of the most flexible proteins that will indeed be part of our study. |
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Thanks for the answers, it is more obvious what Docking project is doing in term of science. Docking@Home is a pure non-profit effort, and we will not make money from the results. We are academic researchers that are funded by public agencies [NSF and NIH] so that we can benefit the public. This is accomplished by publishing our results and methods in peer reviewed scientific journals, releasing our results to the public via this project web site, and eventually by collaborating with other publicly funded experimental researchers. By collaborating with other publicly funded experimental researchers, we hope this will allow us all to get more out of our limited publicly funded research dollars. The only connection between Predictor and Docking is that our project leader Michela Taufer helped to establish the Predictor site in the Charlie Brooks III lab at TSRI, and is now establishing the Docking site in her own lab at UTEP. Predictor is a site for the prediction of protein structure, folding, and structural transitions. Docking is a site for the prediction of protein-ligand interactions using CHARMM based molecular docking methods. |
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Thanks, that answered (not only) my questions very well. |
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Also appreciate the good response and information about the project. Knowing what its about, And having a responsive Adm's Crew, Makes someone like myself who basically runs the wu, and gets another one, Feel like they are really involved.
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Over @Rosetta a question came up regarding the comparability of Docking and Rosetta. This thread, and especially Dr. Armens posts were igven as an explanation.
If anyone can post there could you ask how it compares to the THINK virtual screening/docking as developed by www.treweren.com I'm sure there are a few people that would like to know that of which some HIV protease inhibition can be found here ? Can anyone be so kind to either answer it over there in the relevant thread or just here? |
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Andre Kerstens
Forum moderator Project tester Volunteer tester 
Joined: Sep 11 06 Posts: 749 ID: 1 Credit: 15,199 RAC: 0 |
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I've asked Roger to answer this for you. He said he would soon.
Over @Rosetta a question came up regarding the comparability of Docking and Rosetta. This thread, and especially Dr. Armens posts were igven as an explanation. ____________ D@H the greatest project in the world... a while from now! |
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Over @Rosetta a question came up regarding the comparability of Docking and Rosetta. This thread, and especially Dr. Armens posts were igven as an explanation. As a general policy, I would prefer to not summarize what is done on other life-science BOINC projects, and I would direct you to the Find-a-Drug site ( http://www.find-a-drug.org ) or also to the wikipedia entry ( http://en.wikipedia.org/wiki/Find-a-drug ). To my knowledge, the Find-a-Drug site is now permanently closed as of Dec 2005. However, since we are a new site, I will provide a brief comparison of what has been done in their project and how this compares and contrasts with the scientific goals and methods of our project. Keith Davies ran the project Find-a-Drug and previously the CAN-DDO cancer screening project that was funded by the National Foundation for Cancer Research (NFCR). These projects used the proprietary software THINK (developed by Treweren Consultants - Keith Davies and coworkers) for virtual screening of protein drug targets for various diseases including cancer. Some of the results for the cancer drug targets were then validated using NCI cancer screening data. As there are many different methodological approaches to protein folding, there are also many different approaches to protein-ligand docking. The proprietary software THINK uses a "pharmacophore pattern matching" approach with a full conformational search. This method is able to search rapidly through very large databases of available compounds and as well as computer-generated derivates of available compounds (theoretical compounds). To my knowledge the THINK methodology has not been published in peer-reviewed scientific journal, but the method is summarized in the following publications: Davies, E. K., Glick, M., Harrison, K. N. & Richards, W. G. (2002). Pattern recognition and massively distributed computing. Journal of Computational Chemistry. 23(16): 1544-1550. Davies, E. K. & Richards, W. G. (2002). The potential of internet computing for drug discovery. Drug Discovery Today, 7(11 Suppl): S99-S103. Also, some details about the methods and results from the Find-a-Drug project are available in a pdf from the CCP4 website (Collaborative Computational Project Number 4 in Protein Crystallography). ( http://www.ccp4.ac.uk/maxinf/mm4mx/PDFs/K.Davies.pdf ) The methods that we use for protein-ligand docking are quite different that the pharmacophore pattern matching approach employed by THINK. Our method is likely to be much more accurate, but is also significantly more computationally expensive, and is therefore not as well-suited for searching for very large databases of compounds. We currently use a molecular mechanics all-atom CHARMM-based docking method with fully flexible ligands, and a rigid protein conformation. One of the goals of our project is to develop models to incorporate flexibility into the protein as well, although this is very challenging. The details of the methodology used in our CHARMM-based docking (also known as CDOCKER) and several benchmark tests of docking and scoring have been published in several peer reviewed journal articles (shown below). In terms of the general approach and scientific goals of the project, there are some notable differences between Find-a-Drug and Docking@home. The Find-a-Drug project aimed at virtual screening of very large databases of compounds for specific drug targets with the goal of identifying as many "hits" or drug-like molecules as possible that might lead to new drugs. This approach assumes that the method has sufficient accuracy for a large scale application of the method. We applaud the pioneering work of the Find-a-Drug project, and we also intend to do such large virtual screens in the future. However, we still have a lot of work to do before we can perform virtual screening on such a large scale. Our approach is that we need to spend our efforts on improving our method and its accuracy, and then apply it to specific applications. We also need to develop and improve our databases of compounds. Therefore, our primary scientific goals in the short term are to improve and validate our methodology so we can improve accuracy. This means that we have to carefully examine how our methods perform when we know the answers (benchmark tests). In this way, it is our goal to develop and validate new methods of incorporating protein flexibility into our docking method without compromising the accuracy of our predictions. For example, in a virtual screen it is known that not including protein flexibility reduces accuracy. This is because compounds that are known to bind may not be able to bind given a specific rigid conformation of the protein that does not perfectly accommodate them (these are known as false negatives). Alternatively, introducing protein flexibility in a virtual screen may allow compounds to score well that are known not to bind, or bind with a low affinity (these are known as false positives). If the false positive rate becomes to large, then introducing flexibility into a virtual screen will have little or no benefit. This is a paradox of introducing protein flexibility into protein ligand docking that we intend to study. It is our goal to study various models of incorporating protein flexibility into docking, and to assess their accuracy with regards to this paradox. For this reason, our bench-mark studies will focus on a set of proteins that are known to be flexible. We will also perform example virtual screens where the "answer is known" from experimental high-through-put screening, so we can directly assess the effect of protein flexibility on the number of false positives and false negatives. Finally, because we intend to publish all of our methods and results in peer-reviewed scientific journals, any advancements in methodology will be available to the general public and academic researchers. Selected peer-reviewed scientific journal articles: Taufer, M., Crowley, M., Price, D., Chien, A. A., & Brooks, C. L. III (2005). Study of an accurate and fast protein-ligand docking algorithm based on molecular dynamics. Concurrency and Computation: Practice and Experience. 17(14): 1627-1641. Erickson, J. A., Jalaie, M., Robertson., D. H., Lewis, R. A., & Vieth, M. (2004). Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. Journal of Medicinal Chemistry, 47(1): 45-55. Ferrara, P., Gohlke, H., Price, D. J., Klebe, G. & Brooks, C. L. III (2004). Assessing scoring functions for protein-ligand interactions. Journal of Medicinal Chemistry, 47(12): 3032-3047. Bursulaya, B. D., Totrov, M., Abagyan, R. & Brooks, C. L. III (2003). Comparative study of several algorithms for flexible ligand docking. Journal of Computer Aided Molecular Desing. 17(11): 755-763. Wu, G., Robertson, D. H., Brooks, C. L. III. & Vieth, M. (2003). Detailed analysis of grid-based molecular docking: A case study of CDOCKER- a CHARMm-based MD docking algorithm. Journal of Computational Chemistry, 24(13):1549-1562. Vieth, M., Hirst, J. D., Kolinski, A. & Brooks, C. L. III (1998). Assessing energy functions for flexible docking. Journal of Computational Chemistry, 19(14):1612-1622. Vieth, M., Hirst, J. D., Dominy, B. N., Daigler, H., & Brooks, C. L. III (1998). Assessing search strategies for flexible docking. Journal of Computational Chemistry, 19(14): 1623-1631. |
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I decided to join the project after reading the post by Dr. Armen on september 18th.
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suguruhirahara
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I have a question.
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I have a question. 1tng is the protein... of course we will test with more proteins. As far as number of proteins tested in each phase I don't know... perhaps Andre might know that, I will ask him. |
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Michela
Forum moderator Project administrator Project developer Project tester Project scientist
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Dear All,
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I have a question. Suguruhirahara, Michela provided a great answer to this question. However, I will also add that the protein-ligand complex 1tng is part of one of our test-sets. In the course of our project, we will apply different docking models to try to dock the individual test-case 1tng many times to see how our models perform. Each time we make a change to our model, we will likely see how we perform on 1tng. I myself do not know how many protein-ligand complexes will be tested in the alpha, beta and full-operational phase of our project; the short answer is literally as many as possible. I have been working for months on constructing different test-sets that we will use to test various aspects of our docking methodology. I will keep you updated on our progress in the future. Right now, during the alpha phase, we are performing some preliminary studies and also doing things like error-checking to make sure that we are ready for prime-time. |
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I myself do not know how many protein-ligand complexes will be tested in the alpha, beta and full-operational phase of our project; the short answer is literally as many as possible. This is why yesterday I attached my "core duo" to the project, you'll have nearly one of its core only to test your sets :) You make me think about upgrading the old host to help you more, I hope this project have great fortune! I hope also that this web site gets improved to have a whole well organized section to make us learn something :) |
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suguruhirahara
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I hope also that this web site gets improved to have a whole well organized section to make us learn something :) +1 If this project which studies on a specific field will have documents on the website like Rosetta@home, many people will be interested in it. In fact document which explains a project in detail is one of the most important parts in choosing a project to crunch intensively. ____________ 
I'm a volunteer participant; my views are not necessarily those of Docking@Home or its participating institutions. |
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Andre Kerstens
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Roger and Michela, our science guru's are working on this.
I hope also that this web site gets improved to have a whole well organized section to make us learn something :) ____________ D@H the greatest project in the world... a while from now! |
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Its nice to see some really well explained aims in a projecty. You can have 25% of my 2 machines while they continue to turn out data in a reasonable time. When my Core 2 duo arrives ill give you 25% of that as well. I really really hope it moves quicker than the 2 machines i have on now
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as soon as prior commitments are met ...I'll submit 100% here on behalf of SeriousCrunchers.net |
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Thanks for explanation, very appreaciated. Please provide the same type of comments for POEM@home. Thank you. |
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From my perspective, as an individual who conducted ~10yrs of research on Phosphatidyl-Inositol-3-Kinase (PI3K), mapping of Hepatitis C long-arm epitopes, and stem cell research, but who has worked in the Information Technology field the past 10 yrs, I believe what this site needs is a better description of the benefits of this research with key word usage which stimulates the non-scientific individuals who are trying to decide if they want to contribute TFLOPS to this project. Non-scientific folks have no clue what a ligand is, how it functions or what contributions a ligand provides to the general overall stream of protein research and benefits. Instead, perhaps key words such as RNA and DNA (you know, maybe a little explanation that proteins come from RNA and DNA first) might help set the stage. This might sound trite; however, the common everyday person who owns a computer and wants to contribute does not come from a scientific background (in general) I would argue. Contributing to other projects because they look for extraterrestrial life just sounds BIG and less complicated than a project which deals with protein-ligand computational research. So, again, to recapitulate, I believe the employment of some more common terminology, common descriptions, and explanations which are more readily consumed by the non-scientific community would help to increase the contribution of CPU cycles to the Docking@Home project. |
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Dear eNORMous
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Well, let me see if i can put what our computer is doing right now in layman's terms, since it's kind of a mix:
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Hi J,
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What is the difference between targets ic5p, ice5, 3ptb? They appear identical. Thanks. |
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Hi Morris,
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Right now, I am crunching 1xug workunits. 1xug is not among the listed targets posted on this project's website. I suggest you show on the home page a list of current targets that we are crunching. I also suggest that you provide a detailed description of each target that is being covered so that we can know what we are crunching for. Before I forget, what is 1xug?
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Right now, I am crunching 1xug workunits. 1xug is not among the listed targets posted on this project's website. I suggest you show on the home page a list of current targets that we are crunching. I also suggest that you provide a detailed description of each target that is being covered so that we can know what we are crunching for. Before I forget, what is 1xug? I can understand exactly what you're asking. As a non-biologist type, I know it's very easy to get lost in details (I fall into this category as well). I think I'll work with the project scientists to see if we can get some more information online. I think it would be useful to also see which workunits are currently being crunched. I'll post more details as we decide. Thanks ____________ ~Brian Docking@Home Web Implementation |
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If our computational help will result in getting better drugs to market sooner and at a lower expense, will the lower cost be reflected in the over-the-counter price in the USA and other countries?
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From my perspective, as an individual who conducted ~10yrs of research on Phosphatidyl-Inositol-3-Kinase (PI3K), mapping of Hepatitis C long-arm epitopes, and stem cell research, but who has worked in the Information Technology field the past 10 yrs, I believe what this site needs is a better description of the benefits of this research with key word usage which stimulates the non-scientific individuals who are trying to decide if they want to contribute TFLOPS to this project. Non-scientific folks have no clue what a ligand is, how it functions or what contributions a ligand provides to the general overall stream of protein research and benefits. Instead, perhaps key words such as RNA and DNA (you know, maybe a little explanation that proteins come from RNA and DNA first) might help set the stage. This might sound trite; however, the common everyday person who owns a computer and wants to contribute does not come from a scientific background (in general) I would argue. Contributing to other projects because they look for extraterrestrial life just sounds BIG and less complicated than a project which deals with protein-ligand computational research. So, again, to recapitulate, I believe the employment of some more common terminology, common descriptions, and explanations which are more readily consumed by the non-scientific community would help to increase the contribution of CPU cycles to the Docking@Home project. I concur completely... In trying to promote Docking@home, I have to deal with issues that would be more appropriate if explained on the project pages for members to reference when needed, or to expand their own personal knowledge. Heidi-Ann Kennedy Director Scientific Frontline Team Phoenix Rising 
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Recognized by the Carnegie Institute of Science . Washington D.C. |
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It could even be more simple than explain DNA/RNA/Protein etc. Perhaps a short movie that shows a protein, explains that proteins do most of the chemistry that keep us alive and biology functioning in general.
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Michela
Forum moderator Project administrator Project developer Project tester Project scientist
Joined: Sep 13 06 Posts: 163 ID: 10 Credit: 97,083 RAC: 0 |
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Dear All,
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Please provide the same type of comments for POEM@home. Thank you. From what I've seen, POEM@home is involved mainly in protein folding. If there are any good descriptions there on exactly what proteins and why they want to fold them, they're apparantly in the section of their forums which are in German instead of English. |
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Is Docking@home a splitted project of predictor? Now that the Predictor@home site is no longer reachable, you might want to offer a copy of that web page on your site. |
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Here is the new link of predictor.
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Message boards : Docking@Home Science : What is the main goal of Docking@home ?
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["id"]=>
string(2) "27"
["forum"]=>
string(1) "1"
["owner"]=>
string(3) "100"
["status"]=>
string(1) "0"
["title"]=>
string(39) "What is the main goal of Docking@home ?"
["timestamp"]=>
string(10) "1259599360"
["views"]=>
string(4) "5622"
["replies"]=>
string(2) "43"
["activity"]=>
string(19) "5.6544216546363e-81"
["sufferers"]=>
string(1) "0"
["score"]=>
string(1) "0"
["votes"]=>
string(1) "0"
["create_time"]=>
string(10) "1158233708"
["hidden"]=>
string(1) "0"
["sticky"]=>
string(1) "0"
["locked"]=>
string(1) "0"
}
[1]=>
&string(6) "thread"
[2]=>
&string(13) "views=views+1"
}
}
[2]=>
array(7) {
["file"]=>
string(63) "/boinc/projects/docking/html_v2/user/community/forum/thread.php"
["line"]=>
int(184)
["function"]=>
string(6) "update"
["class"]=>
string(11) "BoincThread"
["object"]=>
object(BoincThread)#3 (16) {
["id"]=>
string(2) "27"
["forum"]=>
string(1) "1"
["owner"]=>
string(3) "100"
["status"]=>
string(1) "0"
["title"]=>
string(39) "What is the main goal of Docking@home ?"
["timestamp"]=>
string(10) "1259599360"
["views"]=>
string(4) "5622"
["replies"]=>
string(2) "43"
["activity"]=>
string(19) "5.6544216546363e-81"
["sufferers"]=>
string(1) "0"
["score"]=>
string(1) "0"
["votes"]=>
string(1) "0"
["create_time"]=>
string(10) "1158233708"
["hidden"]=>
string(1) "0"
["sticky"]=>
string(1) "0"
["locked"]=>
string(1) "0"
}
["type"]=>
string(2) "->"
["args"]=>
array(1) {
[0]=>
&string(13) "views=views+1"
}
}
}
query: update docking.thread set views=views+1 where id=27