fpocketR

<img src="docs/_static/images/fpocketR_logo.png" alt="fpocketR logo" width="250" height="250" />

A CLI tool optimized to find, characterize, and visualize drug-like RNA-ligand binding pockets in RNA structures (static or dynamic).

fpocketR is an RNA-specific wrapper for fpocket 4.0

Documentation: fpocketR ReadTheDocs

Contents

• System Requirements
• Installation
  • Recommended: Bioconda
  • Alternative: Conda + pip
  • Testing your installation
• Quick Start
  • Activate the fpocketR Environment
  • Basic Structure Analysis
  • Secondary Structure Visualization
  • Multistate Analysis
  • Apo/Holo Analysis
  • Additional Arguments
• Demonstration Workflows
• Usage
• Copyright
• Acknowledgements

System Requirements

• Supported platforms: Linux (x86_64), MacOS (Intel/x86_64)
• Not supported: ARM-based MacOS (M1/M2) and native Windows
• Experimental: fpocketR may work on ARM MacOS with fpocket 4.2.1+. WARNING: We had observed that newer version of fpocket (>4.0.3) led to changes in predicted pockets which we have not validated.
• Windows users: Use WSL2 (Windows Subsystem for Linux) to run fpocketR. Follow the install instructions using the WSL2 linux terminal.

Installation

Recommended: Bioconda

fpocketR is now available on Bioconda!

1. Install Conda
   If you don’t have conda, follow the official installation guide.

2. Add the Bioconda channel (if not already added):

   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   

3. Create and activate a new environment with fpocketR:

   conda create -n fpocketR fpocketr
   conda activate fpocketR
   

   This will install all required dependencies, including fpocket and fpocketR.

---

Alternative: Conda + pip

If you prefer to install via PyPI, you can use Conda to set up the environment and then install fpocketR with pip:

1. Create and activate a new environment with fpocket and Python 3.11

   conda create -n fpocketR -c conda-forge fpocket=4.0.3 python=3.11 pymol-open-source=2.5
   conda activate fpocketR
   

2. Install fpocketR and dependencies from PyPI

   pip install fpocketr
   

   Note: The fpocket binary is installed via conda, not pip.

Testing your installation

After installing, you can verify your setup by running the test suite:

1. Make sure you have installed the testing tools:

   pip install 'fpocketR[test]'
   

2. Find the fpocketR install location:

   python -c "import fpocketR; print(fpocketR.__file__)"
   

3. Run pytest in the fpocketR source directory:

   pytest /path/to/fpocketR/
   # or, if you are in the source directory:
   pytest
   

If all tests pass, your installation is working correctly.

Notes:

• For Windows users, use WSL (Windows Subsystem for Linux) for best compatibility. Guide to installing WSL and Ubuntu
• For MacOS users: fpocketR is not compatible with arm-based M1/M2 processors (only Intel/x86).

Quick Start

Run fpocketR from the command line to analyze RNA structures and visualize ligand binding pockets.

Activate the fpocketR Environment

Activate your environment after installing fpocketR and its dependencies:

conda activate fpocketR

Tip: For a full list of options, run:

python -m fpocketR --help

Basic Structure Analysis

Analyze a local PDB file or fetch by PDB ID using the -pdb argument:

python -m fpocketR -pdb 3e5c.pdb
# or
python -m fpocketR -pdb 3e5c

Example output:

| Tertiary structure | Pocket characteristics | | :----------------: | :-------------------: | | <img src="docs/_static/images/3e5c_3D.png" height="150" /> | <img src="docs/_static/images/3e5c_1D.png" height="30" /> |

Pocket color legend:

<img src="docs/_static/images/fpocketR_pocket_color_legend.png" height="60" />

Secondary Structure Visualization

Add a secondary structure diagram using the -ss argument:

python -m fpocketR -pdb 2l1v.pdb -ss 2l1v.nsd

Example output:

| Tertiary structure | Secondary structure | Pocket characteristics | | :----------------: | :-----------------: | :-------------------: | | <img src="docs/_static/images/2l1v_3D.png" height="150" /> | <img src="docs/_static/images/2l1v_2D.png" height="150" /> | <img src="docs/_static/images/2l1v_1D.png" height="30" /> |

Multistate Analysis

Analyze all NMR or Cryo-EM states using the --state 0 argument:

python -m fpocketR -pdb 2l1v.pdb -ss 2l1v.nsd --state 0

Example output:

| Tertiary structure<br>(pocket density) | Secondary structure<br>(pocket density) | Pocket summary<br>(all states) | | :-----------------------------: | :----------------------------------: | :-------------------------: | | <img src="docs/_static/images/2l1v_all_states_3D.png" height="150" /> | <img src="docs/_static/images/2l1v_2D_pocket_density.png" height="150" /> | <img src="docs/_static/images/2l1v_all_states_1D.png" height="70" /> |

Apo/Holo Analysis

Align ligand-bound (holo) and ligand-free (apo) structures for direct comparison using the --alignligand argument:

python -m fpocketR -pdb 8f4o_apo.pdb --alignligand 2gdi_holo.pdb --knownnt 19,20,42,43

Example output:

| Apo structure and pocket | Apo and holo structures aligned | | :----------------------: | :-----------------------------: | | <img src="docs/_static/images/8f4o_apo_3D.png" height="150" /> | <img src="docs/_static/images/8f4o_apo_holo.png" height="150" /> |

Additional Arguments

Customize analysis with optional arguments:

• Select RNA chain: -c (--chain)
• Select ligand: -l (--ligand)
• Set raytracing resolution (lower = faster): -dpi (--dpi)
• Specify output path: -o (--out)

python -m fpocketR -pdb 2gdi_holo.pdb --chain Y --ligand TPP --dpi 10 --out ./TPP_RS

Example output:

• Output files and figures add to custom directory: ./TPP_RS/2gdi_holo_clean_out/.

| Tertiary structure (low resolution) | | :----------------------------------: | | <img src="docs/_static/images/2gdi_holo_3D_10.png" height="150" /> |

Demonstration Workflows

For advanced usage and batch processing, see the example workflows in the /fpocketR/demo folder:

• Batch submission using Bash scripts
• Batch submission using Snakemake
• Multistate analysis on modeled RNA structures from CASP

Each demo includes step-by-step instructions and sample files to help you automate fpocketR analyses for large datasets or complex workflows.

Usage

Full list of arguments for fpocketR.

| Option / Argument | Type | Description | | :---------------------------- | :---------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Input options | | | | -pdb, --pdb (Required) | str | Path to a .pdb file, .cif file, or 4 character PDB identification code. | | -ss, --ss | str | Path to an .ss or other secondary structure file for generating secondary structure figures. | | fpocket parameter options | | | | -m | float |