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A Geant4 based simulation platform of the Holland Proton Therapy Centre (HollandPTC, Netherlands) R&D beamline (G4HPTC-R&D) was developed to enable the planning, optimisation and advanced dosimetry for radiobiological studies. It implemented a six parameter non-symmetrical Gaussian pencil beam surrogate model to simulate the R&D beamline in both a pencil beam and passively scattered field configuration. Three different experimental proton datasets (70 MeV, 150 MeV, and 240 MeV) of the pencil beam envelope evolution in free air and depth-dose profiles in water were used to develop a set of individual parameter surrogate functions to enable the modelling of the non-symmetrical Gaussian pencil beam properties with only the ProBeam isochronous cyclotron mean extraction proton energy as input. This refined beam model was then benchmarked with respect to three independent experimental datasets of the R&D beamline operating in both a pencil beam configuration at 120 and 200 MeV, and passively scattered field configuration at 150 MeV. It was shown that the G4HPTC-R&D simulation platform can reproduce the pencil beam envelope evolution in free air and depth-dose profiles to within an accuracy on the order of ± 5% for all tested energies, and that it was able to reproduce the 150 MeV passively scattered field to the specifications need for clinical and radiobiological applications. • Geant4 was used to develop a simulation platform of the HollandPTC R&D beamline. • A non-symmetrical Gaussian proton pencil beam model was developed and optimised. • Experimental benchmarking done at multiple energies and beamline configurations. • Simulation platform accurately reproduced all experimental measurements. • Simulation platform met specifications for clinical and radiobiological applications. [ABSTRACT FROM AUTHOR]