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