Protein-Ligand Database (PLDB)

An active knowledge base of structural data and protein-ligand interactions

Active and Flexible Data Storage

PLDB complements and improves its users' intuition by helping them to identify trends and patterns in their structural data, and allowing users to ask complex questions like "Is a given interaction seen in experimental structures?" and "What kinds of groups could I add to form a desired interaction?" While PLDB was designed to store structural data, it provides a flexible storage solution that can handle almost any kind of data you may want to associate with a structure, including density maps, WaterMap data, or even pertinent PDF publications.

Fully annotated PDB:
PLDB comes with the entire PDB that has been processed through Schrödinger’s validated workflow. The PLDB's processing pipeline leverages validated Schrödinger technology like Protein Prep Wizard (PPW) and SiteMap to get the most out of the PDB. A curated set of binding affinity ranges is available so that users can track the impacts of structural motifs and interactions on intermolecular forces between ligands and receptors. As new structures are added to the PDB, the PLDB is automatically updated to ensure its dataset is always current.

Advanced searching:
PLDB can not only search by geometric parameters, but also interaction motifs. Users have the ability to search for standard protein-ligand interactions, e.g., hydrogen bonds, pi-pi interactions, salt bridges, etc. Powerful geometric search criteria can be used to mine public and proprietary data for measurements, e.g., distances, angles, centroids, and planes. Custom structural motifs and metadata can be easily parsed from uploaded data and made searchable.

Integrated visualization:
PLDB provides structure visualization tools suited to the varied needs of its users. For those who are most comfortable working in 3D, PLDB is deeply integrated with Maestro. The PLDB's easy-to-use Web GUI empowers users who prefer a lightweight 2D environment by giving them access to Ligand Interaction Diagram. The Web GUI presents the perfect interface for communication between users who think in three dimensions and those that think in two by allowing modelers and crystallographers to run queries in Maestro and then share their results with their chemists on the Web.

Kinase features:
The PLDB comes shipped with a set of kinase structural features such as the gatekeeper residue, C-helix, DFG motif, hinge region, and more, which can be used for visualization as well as searching. All kinases in the PLDB share a structure-based alignment and are aligned automatically when visualized in both Maestro and the Web GUI.

Citations and Acknowledgements

Schrödinger Release 2021-4, Protein-Ligand Database (PLDB), Schrödinger, LLC, New York, NY, 2021.

ö "The Role of Bridging Water and Hydrogen Bonding as Key Determinants of Noncovalent Protein–Carbohydrate Recognition"

Ruvinsky, A.M.; Aloni, I.; Cappel, D.; Higgs, C.; Marshall, K.; Rotkiewicz, P.; Repasky, M.; Feher, V.A.; Feyfant, E.; Hessler, G.; Matter, H., ChemMedChem, 2018, ,
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