
                               M O D E L L E R

       PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                         MODELLER 9.16, 2016/01/07, r10745


                     Copyright(c) 1989-2016 Andrej Sali
                            All Rights Reserved


                           Written by Andrej Sali,
                               with help from
           Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong,
         Marc A. Marti-Renom, Narayanan Eswar, Frank Alber, Maya Topf,
       Baldomero Oliva, Andras Fiser, Roberto Sanchez, Bozidar Yerkovich,
     Azat Badretdinov, Francisco Melo, John P. Overington and Eric Feyfant

                University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                     Harvard University, Cambridge, USA
                  Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


    Andrej Sali, email modeller-care AT salilab.org, web http://salilab.org/



** DESCRIPTION:

  MODELLER is used for homology or comparative modeling of protein three-
  dimensional structures (1). The user provides an alignment of a sequence
  to be modeled with known related structures and MODELLER automatically 
  calculates a model containining all non-hydrogen atoms. MODELLER 
  implements comparative protein structure modeling by satisfaction of
  spatial restraints (2,3), and can perform many additional tasks, including
  de novo modeling of loops in protein structures, optimization of various
  models of protein structure with respect to a flexibly defined objective
  function, multiple alignment of protein sequences and/or structures,
  clustering, searching of sequence databases, comparison of protein
  structures, etc.
  MODELLER is written in Fortran-90 and is meant to run on UNIX, Windows,
  Linux and Apple systems.

  1. M.A. Marti-Renom, A. Stuart,  A. Fiser,  R.Sanchez,  F. Melo,  A. Sali.
     Comparative protein structure modeling of genes and genomes. 
     Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.

  2. A. Sali & T.L. Blundell. Comparative protein modelling by 
     satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

  3. A. Fiser, R.K. Do, A. Sali. Modeling of loops in protein structures,
     Protein Science 9. 1753-1773, 2000.



** DISTRIBUTION:

  MODELLER is available free of charge to academic non-profit institutions
  from the MODELLER website (http://salilab.org/modeller/).

  For commercial or governmental licensing of MODELLER, please contact
  Accelrys Inc., 10188 Telesis Ct., San Diego, CA 92121, USA,
  email support@accelrys.com, http://www.accelrys.com/.



** REGISTRATION and INSTALLATION

  Please access the academic license server from the MODELLER website
  to apply for the MODELLER key. You will need this license key in order
  to run the MODELLER installer. See the file INSTALLATION for installation
  instructions.



** MODELLER USERS EMAIL LIST:

  In addition to the manual, you can receive help from the MODELLER 
  users email list. The archive of this list contains many tips about 
  using MODELLER. You can access it from the MODELLER website at
  http://salilab.org/modeller/ where you will find detailed instructions 
  on how to subscribe yourself. 



** GRAPHICAL INTERFACE:

  MODELLER runs via scripts written in the Python language, and does not provide
  any graphical interface. A graphical interface to MODELLER is available as
  part of Accelrys' InsightII, and Discovery Studio interactive molecular
  modeling programs, which also contain many other tools for protein 
  modeling and structural analysis. These programs facilitate preparation of 
  input files for MODELLER (e.g. alignment file) as well as an analysis of 
  the results (e.g., an evaluation of the models). If you are interested in 
  these programs, please contact Accelrys Inc. at the address above.


** ADDITIONAL INFORMATION:

  Additional information about MODELLER can be obtained on our web site 
  http://salilab.org/.


  Sincerely,

  MODELLER Team
  2016/01/07, r10745.
