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BiKi Basic

Making your life easier for MD simulations
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BiKi Basic is the fundamental module of BiKi Life Sciences, as it provides a user-friendly GUI interface and a toolkit to set-up a molecular dynamics simulation. Thanks to BiKi Basic, the user is guided throughout all the necessary steps of the MD setup. The user can retrieve a structure, calculate the main parameters, build-up the system and launch a run. Post-processing analysis can easily be performed at the end of the simulations. In BiKi Basic is included several utility to manage and analyse your MD simulations, including:

  • Clustering: Extracting relevant conformations from MD trajectories. The significant amount of data generated by Molecular Dynamics runs calls for rationalizing tools to summarize the keys events of a trajectory. The clustering algorithm implemented in BiKi comprises a fully automated protocol to obtain useful and human interpretable stable MD conformations.
  • Pockets: Locating binding site in protein structures. BiKi Life Sciences ships a user friendly interface to NanoShaper to both compute different molecular surface definitions (Solvent Excluded, Gaussian, Skin) and to find the pockets (both solvent exposed and buried sites) in a fully automated way.
  • Residue parametrization: Calculate MD parameters for new residues and ligands. BiKi Life Sciences allows to calculate the charges and all bond information to be used in MD.
  • Trajectory cleaner: Easy way to clean from artefacts the MD simulations. After long simulations, the trajectory could affect by so called “Periodic Boundary Conditions” artefacts by which the molecules are visible “broken” in the box. With this utility the trajectory is easily cleaned.


S. Decherchi et al, BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. J. Chem. Inf. Model.

G. La Sala et al, Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis. ACS Cent. Sci.