DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion

Theelucidation of structural interfaces between proteins and inorganicsurfaces is a crucial aspect of bionanotechnology development. Despiteits significance, the interfacial structures between proteins andmetallic surfaces are yet to be fully understood, and the lack ofexperimental investigation has impeded the development of many devices.To overcome this limitation, we suggest considering the generationof protein/surface structures as a molecular docking problem witha homogenous plan as the target. To this extent, we propose a newsoftware, DockSurf, which aims to quickly propose reliable protein/surfacestructures. Our approach considers the conformational explorationwith Euler's angles, which provide a cartography instead ofa unique structure. Interaction energies were derived from quantummechanics computations for a set of small molecules that describeprotein atom types and implemented in a Derjaguin, Landau, Verwey,and Overbeek potential for the consideration of large systems suchas proteins. The validation of DockSurf software was conducted withmolecular dynamics for corona proteins with gold surfaces and providedenthusiastic results. This software is implemented in the RPBS platformto facilitate widespread access to the scientific community.