structure-based prediction of protein complexes
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README

README

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MODTIE: structure-based prediction of binary and higher-order protein complexes
v1.11. Released Oct 8, 2010.
Copyright 2005,2010 Fred P. Davis
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http://fredpdavis.com/modtie

 MODTIE predicts binary protein interactions and higher-order protein
 complexes from a set of protein sequences based on their similarity to
 template complexes of known structure. It can be used for genome-wide
 prediction, through interaction with the MODBASE database of comparative
 models (http://salilab.org/modbase), or to score individual protein
 complexes. This package contains the software that implements the method.

 MODTIE v1.11 uses:
 * template structures from PIBASE v2010
 * domain definitions from SCOP v1.75


o Using MODTIE
--------------
 This package contains the software used to make predictions using MODTIE.
 Three programs are included for typical prediction purposes:

 1. runmodtie.modbase.pl - Predict interactions between protein sequences
                           using comparative models available in MODBASE

 2. runmodtie.targetstrxs_template.pl - Score interactions between two
                  protein structures given a template complex structure

 3. runmodtie.scorecomplex.pl - Score the structure of a protein complex

 The code is mostly in Perl, with some C code for more expensive computations.
 A users manual is provided describing the installation procedure and three
 typical run modes.


o Downloading MODTIE
--------------------

 The software package is available at http://fredpdavis.com/modtie

 The four data files used by the package are available from Zenodo:
 https://zenodo.org/record/29594

 1. modtie_data.modtie_v1.11.tgz (55 MB)
 2. pibase2010_subsets_residues.modtie_v1.11.tar (519 MB)
 3. pibase2010_bdp_residues.modtie_v1.11.tar (680 MB)
 4. pibase2010_data.modtie_v1.11.tar (425 MB)


o History
---------
 MODTIE was developed at the University of California, San Francisco in the
 laboratory of Andrej Sali (http://salilab.org) and continued at the
 Janelia Research Campus of the Howard Hughes Medical Institute
 (http://janelia.org).

 Changes
 -------
 * v1.11  adjusts for new residue numbering scheme in MODBASE
 * v1.1   upgrade to new PIBASE v2010 and SCOP domains v1.75


o Citing MODTIE
---------------
 If you use the software to predict protein interactions within a single
 species, or to score protein complexes, please cite:

 Protein complex compositions predicted by structural similarity.
 Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS.
 Nucleic Acids Res (2006) 34:2943-2952.


 If you use the software to predict inter-species protein interactions,
 such as host--pathogen interactions, please cite:

 Host-pathogen protein interactions predicted by comparative modeling.
 Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A.
 Protein Sci (2007) 16:2585-2596.


o Contact information
---------------
 Fred P. Davis
 email: fredpdavis@gmail.com
 web:   http://fredpdavis.com


This file is part of MODTIE.

MODTIE is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

MODTIE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with MODTIE.  If not, see <http://www.gnu.org/licenses/>.

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