Title and Overview

GOLD scoring function performance against the Astex Diverse set of protein-ligand complexes: side-by-side comparison with other docking programs Read how GOLD's different scoring functions perform and how GOLD overall fares against other commonly used docking packages. This case study details our results prepared for the Docking and Scoring Symposium at the 241st ACS Meeting in Anaheim.

GOLD scoring function performance against the DUD decoy/active set Read about our findings when exploring which scoring function performs best overall for Virtual Screening applications, and which may be best applied to certain target classes. This case study details our results prepared for the Docking and Scoring Symposium at the 241st ACS Meeting in Anaheim.

Sampling experimentally observed ring conformations during protein-ligand docking Ring structures commonly form the core of small molecule drugs and biological substrates. The problem of exploring conformational space of flexible rings in protein-ligand docking is examined using the program GOLD.

Assessing the reliability of protein-ligand structures A common task in structure-based drug design is the validation of protein-ligand structures. Explore protein-ligand complexes with a view to detecting suspect and/or interesting features.

Identifying new BACE inhibitors from non-homologous structures Identify structures in the PDB that have similar cavities in terms of shape and properties to a cavity of known pharmaceutical interest.

Deriving a receptor based QSAR model using docking data Use GOLD-derived 3D parameters and 2D data to illustrate a quantitative understanding of structure activity relationships of a series of potent serine protease inhibitors.

Integrating Relibase+ information with other data sources See how a major pharmaceutical company integrated structural data from Relibase+ with another database.

Improved docking performance using ensemble docking Read how GOLD's novel approach to docking into multiple protein models, ensemble docking, can reduce the time taken to carry out such experiments and improve your screening results.

Scaffold-hopping and fragment-linking using the Cambridge Structural Database See how the CSD can be used as an "ideas-generator" for novel scaffolds (given an active inhibitor of known binding mode) and good linkers between two binding site fragments.

Validation of Docking Poses via Interaction Motif Searching Compare protein-ligand interaction motifs as a means of separating correct poses from high scoring and incorrect poses.

Identifying and modelling key water molecules See how the PDB and CSD can be used to identify key hydration sites and those that mediate protein-ligand interactions. Also learn how to model water molecules in protein-ligand docking.

Validation of nature and coordination of metals in protein structures by matching against the data in the CSD See how the CSD can be used to identify incorrectly assigned metal atoms in PDB entries.