ProtPOS

ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies.
https://cbbio.online/software/protpos/

Features

lightweight
forcefield independent
output in PDB format
fast and reliable

Project Samples

Lysozyme adsorption on hydrophobic PTFE surface

Project Activity

See All Activity >

License

Other License

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ProtPOS Web Site

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Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Python, Unix Shell

Related Categories

Unix Shell Molecular Science Software, Unix Shell Bio-Informatics Software, Unix Shell Artificial Intelligence Software, Python Molecular Science Software, Python Bio-Informatics Software, Python Artificial Intelligence Software

Registered

2016-04-16

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