nunziati/Gly-pipe

Software for the creation of new protein surface pockets.

Gly-pipe

Software for the creation of new protein surface pockets.

Gly-pipe acts on protein structure files (.pdb) by substituting a heavy amino-acid with a glycine, a process known as glycinization.

Gly-pipe version 1.0

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1. INSTALLATION

Gly-pipe is distributed as a python script and does not need particular installation procedures itself. Simply extract the archive in the destination directory.

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2. DEPENDENCIES

Gly-pipe runs with any python3 or python2 distribution. A python2 distribution is mandatory for version 1 of the SADIC software, python 3.10 is required for the SADIC package (version 2).

SADIC (Simple Atom Depth Index Calculator) is needed in order to calculate atom depth indexes.

• SADIC version 1:
  • It can be retrieved at: http://sadic.sourceforge.net/
  • To install SADIC, a python2 distribution is needed.
  • Numarray package is needed in order to build and install SADIC. Numarray can be downloaded at: https://sourceforge.net/projects/numpy/files/Old%20Numarray/
  • Numarray should be extracted and installed using the "setup.py" script included in the Numarray package.
  • SADIC can then be installed using the "setup.py" script included in the SADIC package.
• SADIC version 2:
  • It can be installed with:

   pip install sadic

POPS (solvent accessible surface areas of proteins and nucleic acids) is needed in order to calculate the SASA of each residue.

• It can be downloaded at: https://github.com/Fraternalilab/POPS
• Documentation is available at: http://fraternalilab.github.io/POPS/

Pymol is needed, in order to mutate and minimize the structures.

• It can be found at: https://pymol.org/2/

Energy minimization is carried out by the "optimize" pymol plugin:

• This is a resource-demanding procedure. It is usually skipped.
• Described and downloadable at: https://pymolwiki.org/index.php/Optimize
• Needs Openbabel to run, the installation instructions can be found at: http://openbabel.org/wiki/Category:Installation

Fpocket software is needed in order to estimate the pockets.

• It can be retrieved at: https://github.com/Discngine/fpocket

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3. USAGE

Gly-pipe can be run as any python script by calling: python GlyPipe.py [args]

• The first arg should be the name of the structure to be analyzed, left out the ".pdb" extension, as explained below.
• The second arg is optional and it should be "v1" or "v2", to choose between the two versions of SADIC. By default, version 1 is used.

To analyze a protein structure, its ".pdb" file should be provided.

• The file must be saved in the "structures" subdirectory.
• Then, to analyze it with GlyPipe just call: python GlyPipe.py [name]
• [name] is the filename of the structure to be analyzed, left out the ".pdb" extension

For instance, if you want to analyze the HEWL (Henn Egg White Lysozime) structure:

• Search it on the PDB (https://www.rcsb.org/) through its pdb identifier "9lyz".
• Download the corresponding pdb structure file ("9lyz.pdb").
• Put the file in the "structures" subdirectory inside your Gly-pipe directory.
• Call: python GlyPipe.py 9lyz
• Using the default parameters in the GlyPipe.py script, you should obtain the following results:

Partial results are available for consultation in the other subdirectories.

• SADIC results, in which atom depth indexes can be found, are stored in "results_sadic".
• POPS results, where the SASA of each residue is stored, are saved in "results_pops".
• Mutant structures are saved in "mutated".
• Minimized vesrions of the mutant structures are saved in "minimized".
• Fpocket results are stored in "results_fpocket".

Energy minimization allows to check the stability of each structure produced by GlyPipe.

• This is a resource-demanding step, and can be deactivated by setting the "do_minimize" parameter to False inside the script.
• Sometimes, results are meaningful also without minimizing the structure.
• GlyPipe can be used to build mutant structures which will be minimized later on a more powerful calculator.
• GlyPipe can bypass this step, by setting the parameter "already_minimized" to True. This works only if all the minimized structure versions exist in the "minimized" directory.
• GlyPipe can be stopped before minimization This is done by setting "mutate_only" to True. The mutant versions can be collected in "mutated" and minimized later and/or on a more powerful calculator. The minimized version of each mutant structure should then be put into "minimized". By setting "already_minimized" to True, GlyPipe will then estimate the pockets inside these structures and calculate their DS.

Fpocket estimation parameters can be changed by modifying the "fpocket_params" string in "GlyPipe.py".

• Some predefined versions are provided as commented lines inside the script.
• To choose your own pocket estimation parameters, check the fpocket manual.
• Changing the pocket estimation parameters significantly will decrease the accuracy of the DS predictor.

Final results are stored in "results_glypipe". Here, the outcome of each glycinization is reported.

• If no pocket was created near the glycinized aminoacid, no further action is needed.
• If a pocket was created, the path to the corresponding mutant structure is given.

An approximate druggability index is given by fpocket (Fpocket's Druggability Score):

• If this value is small (smaller than 0.3), the pocket is almost certainly non-druggable.
• Otherwise, the structure should be analyzed with PockDrug in order to verify its druggability.
• This can be done by uploading the structure (whose path is reported in the results file).
• Alternatively, you can upload just the pocket file to PockDrug. This can be found in the "results_fpocket" subdirectory.

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