Draft

Summary and Background

We present a protocol to extract the surface of a biomolecular cavity for shape analysis and molecular simulations.

We apply and illustrate the protocol on the ribosome structure, which contains a subcompartment known as the ribosome exit tunnel or “nascent polypeptide exit tunnel” (NPET). More details on the tunnel features and biological importance can be found in our previous works.

The protocol was designed to refine the output obtained from MOLE software, but can be applied to reconstruct a mesh on any general point cloud. Hence, we take the point-cloud of atom positions surrounding the tunnel as a point of departure.

1. Pointcloud Preparation: Bounding Box and Voxelization

Bbox: There are many ways to extract a point cloud from a larger biological structure – in this case we settle for a bounding box that bounds the space between the PTC and the NPET vestibule.

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