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University of Cambridge 
Protein Structure Modelling  

Welcome to the RAPPER server

RAPPER is an ab initio conformational search algorithm for restraint-based protein modelling. It has been used for all-atom loop modelling (DePristo et al., de Bakker et al.), whole protein modelling under limited restraints (DePristo et al.), comparative modelling (de Bakker et al., in preparation), ab initio structure prediction, structure validation (Lovell et al.), and experimental structure determination with X-ray and nuclear magnetic resonance spectroscopy (DePristo et al.).

Please join the RAPPER modelling Yahoo! group to keep up to date with the continually evolving RAPPER project.

Web interfaces are available on this website for Ramachandran plot analysis.

Public models and datafiles produced in any of the RAPPER publications are available for download here, including the loop conformations from de Bakker et al., the Cα-trace whole protein models from DePristo et al., and the ensembles of alternate X-ray models from the DePristo et al (2004) paper. You can also fetch the current RAPPER binary for several computer architectures. Finally, we are distributing the sidechain conformer libraries from the Shetty et al. paper here.

For more information, look at some talks about RAPPER, gallery of modelling images, or documentation on the program.

Latest News

  • [April 2007] RAMPAGE returns on-line HERE Other on-line servers should return soon!

  • [January 2007] Relase of V0.1 of RAPPERtk a versatile toolkit for conformational sampling under restraints. Try it our from at downloads page. Information for running rtk can be found at the documentation page

  • [January 2007] The new server and cluster have now been purchased and we should have the services back on-line by the end of January / begining of February. Sorry for the delay. If you require RAMPAGE services this will be available from CCP4 soon.

  • [16 August 2006] Knowledge-Based Real-Space Exporations for Low-Resolution Structure Determination has been publised in this months addition of Structure.

  • [August 2006] Unfortunately our server has now died but we have now moved to new server. It will take some time to re-establish the services of loop building, c-alpha trace an RAMPAGE. Hopefully these will come on line soon. Apologies for any inconvenience. All downloads and documentation should still be available. If you are having any problems then plase contact the RAPPER team.

  • [11 May 2006] We have been experiencing problems with the raven server. Consequently the web site has been intermittently unavailbale. We are sorry for this and are moving over to a new server. This means that emails will NOT be able to be sent when a job has been completed. We recomend that you bookmark the results page and make a note of the job id. Hopefull the transition to the new server will be fully complete in a few weeks.

  • [9 March 2006] Is One Solution Good Enough? Check out our recent letter in Nature Strucutural & Molecular Biology with Tom Terwilliger (see below) about representing crystallographic models as ensembles of solutions.

  • [19 January 2006] We are currently experiencing heavy usage of the RAPPER on-line loop and C&alpha modules. This will mean a delay in returning the results. Thank you for your understanding and please be patient.

  • [23 September 2005] Have questions about RAPPER? Find things confusing? Take a look at the RAPPER FAQ for answers to common questions.

  • [19 September 2005] You can now search the RAPPER website for information courtesy of Google

  • [18 September 2005] We've created a RAPPER modelling Yahoo! group for users comments, feedback, questions, and RAPPER-related announcements. Please join to keep up to date as the evolving RAPPER project.

  • [13 September 2005] The Structure (2005) paper detailing X-ray refinement with RAPPER is available (see below). See the RAPPER X-ray refinement HOW-TO for instructions on performing refinement with RAPPER.

  • [12 May 2005]THE Cα-TRACE AND LOOP MODELLING SERVERS ARE NOW BACK ON LINE

  • [3 March 2005] X-ray refinement models used in Crystallographic refinement by knowledge-based exploration of complex energy landscapes are available from the downloads page.

  • [17 February 2005] RAPPER ensembles used in Simultaneous determination of protein structure and dynamics published in Nature. See references below for more information

  • [26 May 2004] Need help running RAPPER for X-ray crystallographic calculations like map fitting and refinement? Take a look at the X-ray calculations HOW-TO.

  • [12 May 2004] The X-ray structure fitting and accuracy paper has been published in Structure. See references below for more information.

  • [2 February 2004] Added a section about the people involved in the RAPPER project.

  • [31 October 2003] Another RAPPER paper is in press. Check out the Shetty et al. paper on fine-grained sidechain conformer libraries.

  • [23 May 2003] The models generated in the our Cα-trace modelling paper (see Reference) are available for download.

  • [23 May 2003] We've updated the RAPPER installation on the webserver to the newest version of RAPPER (v. 0.10 from v. 0.6).

  • [23 May 2003] We've added a web interface to the Cα-trace modelling suite. Click here to go to RAPPER Cα-trace modelling.

  • [14 April 2003] Coming soon: We will soon upgrade the RAPPER installation on the webserver to the newest version of RAPPER (v. 0.10 from v. 0.6). This will include many bug fixes, new algorithms for sampling, and greatly improved performance of both RAPPER and energy-calculations.

  • [14 April 2003] Several bug fixes have been made to the loop.php scripts. The server should now trap more problems with target submissions.

  • [3 October 2002] RAMPAGE is now online. RAMPAGE is a structure validation tool for the assessment of the Ramachandran plot of proteins. Click here to go to RAMPAGE.

  • [20 August 2002] A more recent version of the RAPDF all-atom statistical potential, kindly provided by Dr Ram Samudrala, is now implemented.

  • [20 August 2002] Our Sidechain Conformer Libraries (SCL) for all-atom modelling will be made available shortly.

  • [20 August 2002] Cis peptide modelling is now fully functional.

Authors

RAPPER is developed by Paul de Bakker (now at Massachusetts General Hospital and the Broad Institute, Boston), Mark DePristo, Reshma Shetty (now in the Biological Engineering Division at M.I.T.), Nick Furnham and Swanand Gore in the Crystallography and Bioinformatics Group headed by Tom Blundell. Click here for a picture of Paul and Mark, taken outside the Sanger building during the summer of 2002.

RAMPAGE is developed by Paul de Bakker and Simon Lovell in collaboration with the Richardson's Group at Duke University.

References

  • N. Furnham, Andrew S. Dore, Dimitri Y. Chirgadze, Paul I. W. de Bakker, M.A. Depristo and T. L. Blundell, . (2006) Knowledge-Based Real-Space Exporations for Low-Resolution Structure Determination Structure 14 (8) 1313-1320. [Medline] [PDF ]

  • N. Furnham, T. L. Blundell, M.A. Depristo, T. C. Terwilliger. (2006) Is one Solution Good Enough? Nature Structural & Molecular Biology 13 (3) 184-185. [Medline] [PDF ] [Responce by Helen Burman]

  • M.A. Depristo, P.I.W. de Bakker, R.J. Johnson, T. L. Blundell. (2005) Crystallographic refinement by knowledge-based exploration of complex energy landscapes. Structure 13 (9) 1311-1319. [Medline] [PDF] [Commentary by Randy Read]

  • Kresten Lindorff-Larsen, Robert B. Best, Mark A. DePristo, Christopher M. Dobson & Michele Vendruscolo (2005) Simultaneous determination of protein structure and dynamics. Nature 433 (7022) 128-32. [Medline] [PDF (293.59 KB)]

  • M.A. DePristo, P.I.W. de Bakker, T.L. Blundell (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure (Camb). 12:831-838 [Medline] [PDF (280.16 KB)] [Commentary by Jane Richardson]

  • R.P. Shetty, P.I.W. de Bakker, M.A. DePristo, T.L. Blundell (2003) The advantages of fine-grained side chain conformer libraries. Protein Engineering. 16:963-969 [Medline] [PDF (173.61 KB)]

  • M.A. DePristo, P.I.W. de Bakker, R.P. Shetty, T.L. Blundell (2003) Discrete restraint-based protein modeling and the Cα-trace problem. Protein Science.12:2032-2046 [Medline] [PDF (251.4 KB)]

  • M.A. DePristo, P.I.W. de Bakker, S.C. Lovell, T.L. Blundell (2002) Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles. Proteins Struct. Funct. Genet. 51:41-55 [Medline] [PDF (408.48 KB)]

  • P.I.W. de Bakker, M.A. DePristo, D.F. Burke, T.L. Blundell (2002) Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins Struct. Funct. Genet. 51:21-40 [Medline] [PDF (2.09 MB)]

  • S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Struct. Funct. Genet. 50:437-450 [Medline] [PDF (787.26 KB)]
© 2001-2006 The RAPPER Team 
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