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Membrane protein orientation using a genetic algorithm and knowledge-based statistical potential [bioinformatics]
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timnugent/memembed
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Membrane protein orientation using a knowledge-based statistical potential (c) Tim Nugent 2013 Paper ----- For full details, see http://www.biomedcentral.com/1471-2105/14/276/ Compiling --------- Tested under Ubuntu 13.04 and CentOS 5.4. Requires Boost headers and libraries - specifically boost_thread and boost_system. On recent Debian/Ubuntu distributions, install these packages: libboost-thread1.49-dev libboost-thread1.49.0 libboost-system1.49-dev libboost-system1.49.0 or just install them all: libboost-all-dev Then to compile, just run make (then optionally, make test). Examples -------- For a full list of command line paramaters run with a -h flag. Orientate alpha-helical target using a genetic algorithm: bin/memembed examples/3o7qA.pdb Orientate alpha-helical target using a grid search and 8 threads: bin/memembed -s 1 -a 8 examples/3o7qA.pdb Orientate alpha-helical target using a direct search: bin/memembed -s 2 examples/3o7qA.pdb Orientate beta-barrel target using a genetic algorithm and 8 threads: bin/memembed -b -a 8 examples/2iahA.pdb Orientate alpha-helical target with external N-terminal target using a genetic algorithm, repeating 5 times and retaining the lowest energy orientation, and printing standard error statistics: bin/memembed -s 3 -n out examples/2x2v.pdb Orientate, pre-positioning using topology, and calculate hydrophobic thickness: bin/memembed -t 4-26,46,68 -n out -q 1 examples/2x2v.pdb Calculate helix tilt angles: bin/memembed -z -t 4,26,46,68 -n out examples/2x2v_EMBED.pdb Orientate target using a specific potential file (see supplementary data for cross-validated potential files): bin/memembed -m examples/2iahA.pot examples/2iahA.pdb Mempot ------ To generate potential files to use with the -m flag, use bin/mempot. Edit the TARGETS file to indicate which chain from each PDB file should be parsed from a directory of pre-positioned PDB files, e.g. pdbs/ bin/mempot -l TARGETS -p pdbs/ > alpha.pot Use the file alpha.pot with memembed Scripts ------- Both require Pymol to be installed. Random rotation and translation: scripts/pymol_rotate.py examples/3o7qA.pdb examples/3o7qA_rotated.pdb Generate image: scripts/pymol_membrane_image.py examples/3o7qA_EMBED.pdb examples/3o7qA_EMBED.png You can add some Pymol api commands around line 26. Defaults to 2 threads (line 12) Help ---- Please report bugs and suggestions to: timnugent@gmail.com
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Membrane protein orientation using a genetic algorithm and knowledge-based statistical potential [bioinformatics]