POVME (POcket Volume MEasurer) is an open-source tool designed for detailed analysis of ligand-binding pocket shapes and volumes in proteins. Initially developed to support structure-guided drug discovery, POVME has been widely adopted for its simplicity, speed, and flexibility.
Binding pockets are critical for understanding protein-ligand interactions, a central theme in rational drug design. Pocket shape and volume influence ligand binding, specificity, and the dynamics of molecular recognition. By enabling precise volume and flexibility measurements, POVME has become an essential tool for characterizing these properties in applications such as:
- Identifying and analyzing transient binding pockets.
- Supporting virtual screening and druggability predictions.
- Comparing conformational ensembles from molecular dynamics simulations.
We use pixi to manage Python environments and simplify the developer workflow.
Once you have pixi installed, move into POVME directory (e.g., cd POVME) and install the environment using the command
pixi installNow you can activate the new virtual environment using
pixi shellTo install the latest development version of povme, follow these steps.
Clone the repository.
git clone https://github.com/durrantlab/POVMENavigate into the cloned directory.
cd POVMEInstall the development version using pip.
pip install .This will install povme along with all required dependencies into your current Python environment.
To install a specific version of povme, such as v2.2.2, follow these steps.
Clone the repository and check out the desired version tag.
git clone https://github.com/durrantlab/POVME
cd POVME
git checkout v2.2.2Install the tagged version using pip.
pip install .This will install the specified version of povme and its dependencies into your current Python environment.
If you use POVME in your work, please cite:
- Durrant, J.D., L. Votapka, J. Sørensen, and R. E. Amaro (2014). "POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics." J. Chem. Theory Comput. 10(11):5047-5056.
- Durrant, J. D., C. A. de Oliveira, et al. (2011). "POVME: An algorithm for measuring binding-pocket volumes." J Mol Graph Model 29(5): 773-776.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.