Prot2Surf: fast analysis of protein–surface binding modes
TL;DR
Prot2Surf was tested using catalytic domains of the lytic polysaccharide monooxygenases, interacting with native surfaces, showing that the software can efficiently analyze key binding features, including protein–surface distances, distances between catalytically reactive atoms, and the orientation angle between surface chains and the protein.
Abstract
Summary Prot2Surf is a software tool designed for the characterization and prediction of protein association to surfaces. In this application note, Prot2Surf was tested using catalytic domains of the lytic polysaccharide monooxygenases (LPMOs), interacting with native surfaces. The results show that the software can efficiently analyze key binding features, including protein–surface distances, distances between catalytically reactive atoms, and the orientation angle between surface chains and the protein. These features are essential for distinguishing productive binding poses in these protein–surface systems and for understanding interaction patterns that provide guidance on protein engineering. Prot2Surf performs these analyses within seconds to a few minutes, providing a fast and accessible framework to post-process and characterize protein-surface encounter complexes. Availability and implementation Prot2Surf, which is written in Fortran90, is documented and freely available as open source on GitHub: https://github.com/TUNNELING-GROUP/Prot2Surf. In order to run Prot2Surf, users should also install the SDA software package which is freely available at https://www.h-its.org/downloads/sda7/.