ProtPOS: a python package for the prediction of protein preferred orientation on a surface

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Abstract

Summary: Atomistic molecular dynamics simulation is a promising technique to investigate the energetics and dynamics in the protein–surface adsorption process which is of high relevance to modern biotechnological applications. To increase the chance of success in simulating the adsorption process, favorable orientations of the protein at the surface must be determined. Here, we present ProtPOS which is a lightweight and easy-to-use python package that can predict low-energy protein orientations on a surface of interest. It combines a fast conformational sampling algorithm with the energy calculation of GROMACS. The advantage of ProtPOS is it allows users to select any force fields suitable for the system at hand and provide structural output readily available for further simulation studies.

Availability and Implementation: ProtPOS is freely available for academic and non-profit uses at http://cbbio.cis.umac.mo/software/protpos

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact: shirleysiu@umac.mo

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