fpocketR 1.2.0

Find, characterize, and visualize drug-like pockets in RNA structures.

fpocketR

fpocketR is a modified version of fpocket 4.0 and is optimized for finding, characterizing, and visulizing drug-like RNA-ligand binding pockets.

Installation with Conda

Windows Users: guide to install WSL and Ubuntu

1. fpocketR requires a Unix/Linux to run properly, this means that Windows users need to activate the Windows Subsystem for Linux (WSL).

   • Guide to installing WSL and Ubuntu

Guide to install conda

2. Follow guide to install conda.

   • Windows WSL users: Use Linux installation guide.

Install fpocketR

NOTE for MacOS users: fpocketR is not compatible with arm-based M1 or M2 processors (only intel (x86) processors).

3. Open your terminal and navigate to the directory where you would like to install the fpocketR package (optional).

    cd <path-to-GitHub-reposities>
   

   • Tip for new Windows WSL users: You can navigate to your Windows file system in the WSL command line by using the following command:

     cd /mnt/c/Users/<your-user-name>
     

4. Clone the RNAvigate and fpocketR GitHub repositories.

    git clone https://github.com/Weeks-UNC/fpocketR.git
   

5. Create fpocketR conda environment and install fpocketR and RNAvigate.

    cd fpocketR
    conda env create --file environment.yml
    conda activate fpocketR
    conda develop .
   

Demo / Tutorial

Demonstration of fpocketR usage

Usage

Input options	Description
-pdb, --pdb STRING (Required)	Specify a path to a .pdb/.cif file, or a 4 charater PDB indentification code.
-ss, --ss STRING	Specify an .nsd file or other secondary structure file to generate a secondary structure figure.

fpocket parameter options	Description
-m, --m FLOAT	Sets fpocket -m flag. Minimum radius for an a-sphere. (Default: 3.0)
-M, --M FLOAT	Sets fpocket -M flag. Maximium radius for an a-sphere. (Default: 5.7)
-i, --i INT	Sets fpocket -i flag. Minimum number of a-spheres per pocket. (Default: 42)
-D, --D FLOAT	Sets fpocket -D flag. alpha sphere clustering distance for forming pockets. (Default: 1.65)
-A, --A INT	Sets fpocket -A flag. Number of electronegative atoms required to define a polar a-sphere (Deafult: 3).
-p, --p FLOAT	Sets fpocket -p flag. Maximum ratio of apolar a-spheres. (Default: 0)

Output options	Description
-o, --out STRING	Path to output parent directory. (Default: fpocketR_out_)
-n, --name STRING	Output filename prefix and output subdirectory name. (Default: None)
-y, --yes BOOLEAN	Overwrites output files and directories with same name. (Default: False)

Analysis options	Description
-s, --state INT	PDB states/model for analysis. Set to 0 for all. (Default: None)
-c, --chain STING	Chain(s) IDs conatining RNA (case sensitive). List upto 2 chains seperated by a comma (eg. A,B). (Default: A)
-l, --ligand STRING	PDB ligand identification code (≤ 3 characters).
-lc, --ligandchain STRING	Chain containing the ligand of interest. (Default: )
-nt, --knownnt PARSE_INT	List residue indexes of nts in known pocket (e.g. 1,2,3). Known pockets must contact ≥ 3 of the residues. (None).
-off, -offset INT	Offset between the RNA sequence and PDB structure. offset = starting index of the PDB sequence - 1 (Default: automatic)
-qf, --qualityfilter FLOAT	Minimum fpocket score for a pocket to pass the quality filter. (Default: 0.0)

Figure settings	Description
-dpi, --dpi INT	Specify 3D figure resolution (dots per linear inch). (Default: 300)
-zoom, --zoom INT	Specify zoom buffer distance (Å) to set the feild of view for 3D figures. (Default: 10)
-cp, --connectpocket BOOLEAN	Visually connects pockets in 2D figures. (Default: False)
-al, --alignligand BOOLEAN	Align output structures to input structure. Useful for multistate analysis. (Default: True)