Welcome to Dynamite!

© Benjamin Hall, Paul Barrett and Martin Noble 2005

Example: MDM2 oncoprotein



Contents


About Dynamite

  • What is it?

    Dynamite is a free web-based service that predicts protein motions. It takes as input a pdb file. In return you get various movies and other representations of the protein's motions.

    PLEASE: read the instructions below before diving in. It is not hard to use but failing to carry out some simple instructions will mean you do not get useful results and will waste the available processing power of the facility.

  • How does it work..(but spare me the details)?

    An ensemble of structures is generated. This ensemble is analysed to see what moves together and in which direction. The resulting analysis is visualised and the visualisation is captured either as MPEGs or as scripts for a visualisation program.

    • Custom code accepts and manages jobs and performs the new analysis.
    • The ensemble is generated using Concoord (de Groot et al, below)
    • The analysis is done using Gromacs (Lindahl et al, below) and scripts I have developed here.
    • Visualisation is on VMD (Humphreys et al. below) using scripts that I have written for the purpose.


  • Reliability of results.

    Beware: The results you can get back from Dynamite are based on Simulations. Even worse: they are simulations in which a major shortcut has been taken (a non-Newtonian method of ensemble generation has been used). If Dynamite suggests a motion, this does not prove your protein's motion is really like this.

    ...but...

    it can be a very useful guide, and studies have shown (e.g. de Groot et al; Barrett et al; below) that the results are often rather similar to what is achieved by more rigorous simulations which take months to run.

    In summary, Dynamite can provide you with suggestions about how a protein's dynamics may work. You can use these suggestions to guide your own research. We feel the value of this service is that you can get these results with just a few minutes work on your behalf, and you don't need to spend months learning Molecular Dynamics to do so.



  • How to acknowledge this service

    We do not charge for this service. We just ask that you cite the following paper to acknowledge the service in any publications that make use of it. This will make it easier for us to get grants maintain the service. In particular if it is popular we will need to provide more processing power to keep the turn around time acceptable.

    • Barrett C.P., Hall B.A, Noble, M.E.M. Dynamite: A Simple Way to Gain Insight into Protein Motions Acta Crystallographica D Vol 60 Issue 12-1 pp2280-2287

    In addition this service is based upon several other software packages, all linked together. The nice people who wrote them have allowed us to make this service publicly available at no charge. Please acknowledge this contribution by citing the following references.

    • Lindahl E, Hess B, Spoel Dvd: GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 2001, 7:306-317.

    • de Groot BL, van Aalten DM, Scheek RM, Amadei A, Vriend G, Berendsen HJ: Prediction of protein conformational freedom from distance constraints.Proteins 1997, 29:240-251.

    • Humphrey W, Dalke A, Schulten K: VMD: visual molecular dynamics.J Mol Graph 1996, 14:33-38, 27-38

    You can download the consituent programs from the following addresses [NOTE: you don't need these to use the service: they are included for your convenience in case you want to do your own simulations]





  • OK, OK, Just tell me how to use it!

    1. Edit your PDB file so that it will work properly. Here's how
    2. Submit the PDB here


  • Getting and interpreting your results

    When your job is complete you will be sent an email telling you how to pick them up. Your results will be several Megabytes in size.

    For details on how to get and use your results, click here.



  • Who is responsible for providing this service?
    Mr B.A Hall and Dr M.E.M Noble
    Department of Biochemistry
    University of Oxford
    Oxford
    OX1 3QU
    email: hall AT biop.ox.ac.uk..... replace "AT" with @



  • Acknowledgements We would like to thank the authors of CONCOORD, especially Bert de Groot, the authors of GROMACS, especially Berk Hess, the curator of DSSP, Gert Vriend, and the authors of VMD for permission to implement their software in the Dynamite server. We would also like to thank the group of Mark Sansom, especially Oliver Beckstein and Kaihsu Tai, for helpful discussions about simulation techniques. Thanks to Ben Hall who helped with the validation of the service by comparing results with more rigorous Molecular Dynamics simulations. Paul Barrett is supported by the BBS-RC through a grant to the Oxford Centre for Molecular Sciences.


    The porcupine representation is a development of that published in Kaihsu Tai, Tongye Shen, Richard H. Henchman, Yves Bourne, Pascale Marchot, J. Andrew McCammon (2002)Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J. Am. Chem. Soc. 124:6153-6161 http://dx.doi.org/10.1021/ja017310h

  • Disclaimer
    This service is provided free of charge with no warranty. The user assumes the entire risk related to its use of this service and the data arising from its use. Access to the site may be interrupted, restricted or delayed for any reason. To the full extent permissible by law, we disclaim all responsibility for any damages or losses (including, without limitation, financial loss, damages for loss in business projects, loss of profits or other consequential losses) arising in contract, tort or otherwise from the use of or inability to use the Site, or from any action or decision taken as a result of using Dynamite or these pages.

    We can provide no guarantee that the data you submit will not become public: it is not hard to access other people's results on the postboard. If you are not prepared to risk your PDB data becoming public then DO NOT USE THIS SERVICE.



Benjamin Hall, September 2005 (hall AT biop.ox.ac.uk replace "AT" with @ )

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