Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite

Macromolecular 3D structure is critical in understanding the function and mechanism of biomacromolecules. Recent advances in 3D structure determination techniques have facilitated the study of large macromolecular machines, leading to a rapid increase in the number, size, and complexity of biomacromolecular structures available in the Protein Data Bank (PDB). Facilitating data mining of this large data set will not only help in addressing the challenges in translational research but also allow improved understanding of biological systems. The LiteMol suite offers an innovative approach to data archiving (BinaryCIF), data delivery (CoordinateServer and DensityServer), and 3D molecular visualization (LiteMol Viewer). The newly developed Molecular Query Language (MolQL) enables describing substructures in macromolecules using a wide range of expressions, including the support for Jmol, PyMol, and VMD selections; and the ability to extract data based on structural relationship between individual parts of the molecule. Together, these technologies allow users to mine the 3D structural data in the PDB (e.g., ligand binding sites) by providing a user friendly web based interface to aid translational research and make it easier for non experts to assess and exploit 3D macromolecular structure information. Visit litemol.org and molql.org for more information.