Optimizing Shape Complementarity Scoring Parameters for Recognition of Authentic Protein Crystal Packing Arrangements

摘要

The prediction of protein crystal packing arrangements and the de novo design of new crystal forms are notoriously challenging problems. For both problems, it is useful to enumerate high quality packing arrangements. To efficiently enumerate candidate crystal forms, we have adapted grid-based fast Fourier transform strategies first developed in the context of protein docking algorithms. To maximize performance of the grid-based, shape-complementarity scoring scheme, we have optimized parameters for the recognition of authentic protein crystal packing arrangements. To this end, extensive calculations were performed to assess a wide range of grid representation parameter spaces for a panel of low-solvent protein crystals. The optimum parameters obtained from the computations successfully identify authentic protein crystal packing arrangements out of large pools of similar decoy packing arrangements.