%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % % Predicting Protein Interaction Interfaces with DFE-CRF % % % % Author: Torsten Wierschin % % Universitaet Greifswald % % Institut fuer Mathematik und Informatik % % 17497 Greifswald % % Fon: +49 3834 864624 % % torsten.wierschin@uni-greifswald.de % % % % Date: June 16th, 2014 % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1. INTRODUCTION 2. INSTALLATION 3. PREDICTING PROTEIN INTERFACES 4. TRAINING PARAMETERS 5. CONTACT 1. INTRODUCTION --------------- The tool dfe-crf allows the prediction of interface residues given the structure of a target protein together with signals that are computed from the residue types and the atomic configuration of the neighbourhood at each residue. Further, parameter training is available from the same command line tool as it is explained in the paper "Combining features in a graphical model to predict protein interaction sites" (submitted). 2. INSTALLATION --------------- 1. unpack >tar xzfv dfe-crf.1.0.tar.gz The tar-archive contains: - directory 'dfe-crf.1.0' - file project.root - file makefile.init - file makefile - file README 2. edit the files project.root (general path information) and makefile.init (tool paths) Install dependencies: - Boost C++ Library: source code is tested with version 1.40.0 (filesystem, regex) - libDAI C++ Library: source code is tested with version 0.3.0 compile with > make all 3. PREDICTING PROTEIN INTERFACES --------------------------------- An example script for the tool invocation in order to predict interface residues is available in subdirectory: predict. Executing the binary without options or with '-help' prints an extensive parameters description. 4. TRAINING THE PARAMETERS --------------------------- An training script to tune the DFE-CRF model is contained in subdirectory: train. 5. CONTACT ----------- In case you find a bug, or miss a desireable feature or need executables for a different platform, need detailed info about the model, please write an e-mail to: torsten [dot] wierschin [at] gmail [dot] com