SBILib: a handle for protein modeling and engineering

Abstract

Summary: The SBILib Python library provides an integrated platform for the analysis of macromolecular structures and interactions. It combines simple 3D file parsing and workup methods with more advanced analytical tools. SBILib includes modules for macromolecular interactions, loops, super-secondary structures, and biological sequences, as well as wrappers for external tools with which to integrate their results and facilitate the comparative analysis of protein structures and their complexes. The library can handle macromolecular complexes formed by proteins and/or nucleic acid molecules (i.e. DNA and RNA). It is uniquely capable of parsing and calculating protein super-secondary structure and loop geometry. We have compiled a list of example scenarios which SBILib may be applied to and provided access to these within the library.

Availability and implementation: SBILib is made available on Github at https://github.com/structuralbioinformatics/SBILib.

Figure 1.

A technical demonstration of SBILib’s grafting function. (A) Anti-HIV-1 antibody 17B (pdb:2I5Y) chain L grafted (red) and ungrafted (light blue) superimposed, and ANTI-P185-HER2 ANTIBODY 4D5 (pdb:1FVC) chain A (dark blue). Due to structural identity only the 2I5Y loop and a few flanking residues are shown in the superimposition (light blue). The light chain loop 1FVC:A:19–38 (orange) was grafted in the place of the light chain loop 2I5Y:L:19–38 (beginning and end marked with black arrows) to produce a grafted protein (red). (B) Workflow followed to produce the grafted protein.