Memembed

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